Handbook of Algal Biofuels: Aspects of Cultivation, Conversion, and Biorefinery

Handbook of Algal Biofuels: Aspects of Cultivation, Conversion and Biorefinery comprehensively covers the cultivation, harvesting, conversion, and utilization of microalgae and seaweeds for different kinds of biofuels. The book addresses four main topics in the algal biofuel value-chain. First, it explores algal diversity and composition, covering micro- and macroalgal diversity, classification, and composition, their cultivation, biotechnological applications, current use within industry for biofuels and value-added products, and their application in CO2 sequestration, wastewater treatment, and water desalination. Next, the book addresses algal biofuel production, presenting detailed guidelines and protocols for different production routes of biodiesel, biogas, bioethanol, biobutanol, biohydrogen, jet fuel, and thermochemical conversation methods. Then, the authors discuss integrated approaches for enhanced biofuel production. This includes updates on the recent advances, breakthroughs, and challenges of algal biomass utilization as a feedstock for alternative biofuels, process intensification techniques, life cycle analysis, and integrated approaches such as wastewater treatment with CO2 sequestration using cost-effective and eco-friendly techniques. In addition, different routes for waste recycling for enhanced biofuel production are discussed alongside economic analyses. Finally, this book presents case studies for algal biomass and biofuel production including BIQ algae house, Renewable Energy Laboratory project, Aquatic Species Program, and the current status of algal industry for biofuel production.

Handbook of Algal Biofuels offers an all-in-one resource for researchers, graduate students, and industry professionals working in the areas of biofuels and phycology and will be of interest to engineers working in renewable energy, bioenergy, alternative fuels, biotechnology, and chemical engineering. Furthermore, this book includes structured foundational content on algae and algal biofuels for undergraduate and graduate students working in biology and life sciences.

• Provides complete coverage of the biofuel production process, from cultivation to biorefinery
• Includes a detailed discussion of process intensification, lifecycle analysis and biofuel byproducts
• Describes key aspects of algal diversity and composition, including their cultivation, harvesting and advantages over conventional biomass

• Language: English
• Publisher: Elsevier Science
• Release date: Dec 2, 2021
• ISBN: 9780128241813

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Chapter 1

Cyanoprokaryotes and algae: classification and habitats

Abdullah A. Saber¹, Ahmed A. El-Refaey², Hani Saber³, Prashant Singh⁴, Sanet Janse van Vuuren⁵ and Marco Cantonati⁶,    ¹Botany Department, Faculty of Science, Ain Shams University, Cairo, Egypt,    ²Algae Lab, Botany and Microbiology Department, Faculty of Science, Al-Azhar University, Cairo, Egypt,    ³Department of Botany and Microbiology, Faculty of Science, South Valley University, Qena, Egypt,    ⁴Laboratory of Cyanobacterial Systematics and Stress Biology, Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, India,    ⁵Unit for Environmental Sciences and Management, North-West University, Potchefstroom, South Africa,    ⁶MUSE–Museo delle Scienze, Limnology & Phycology Section, Corso del Lavoro e della Scienza 3, Trento, Italy

Abstract

Cyanoprokaryotes (or cyanobacteria), the most ancient photoautotrophs on Earth, and eukaryotic algae are present nearly in all biomes across the globe. Besides their key role in the production of most of the global net oxygen, they also play multiple pivotal ecological roles in the environments they colonize. Most cyanoprokaryotes and algal species present a high degree of morphological and physiological adaptation to their biotopes. During recent decades, with the affirmation of the polyphasic approach and robust support from molecular phylogenetics, cyanoprokaryotes and algae have undergone extensive taxonomic revisions, resulting in the discovery and description of many new species, genera, families, and orders. In this chapter, we discuss the foundations and modern criteria of cyanobacterial and algal classification. Habitats of cyanoprokaryotes and algae, including extremophiles from hot springs, are presented with a focus on biogeographically and environmentally restricted flagship morphotaxa.

Keywords

Cyanoprokaryotes; microalgae; taxonomic classifications; distributional patterns; flagship species; hot and mineral springs

1.1 Introduction

Algae, including the evolutionarily primitive photoautotrophic cyanoprokaryotes, colonize all abiotic components of planet Earth, namely, air, land, and water. This highly heterogeneous group of organisms is indeed of universal distribution. Most species are morphologically and physiologically adapted to the biomes in which they live. Although many species can live in aerial and terrestrial environments, they are by far the most abundant in aquatic habitats [1]. Starting from the late nineteenth century onwards, the taxonomy of cyanobacteria and algae has been punctuated by a series of major breakthroughs. Great progress during the last century has been fostered by the advent of the electron microscope technique, which led to many new discoveries such as detailed structures of plastids and flagella [2,3]. The development of molecular and phylogenetic tools throughout recent decades not only refined our understanding of the immense diversity of cyanobacteria and algae but also enabled a revolution of ideas with regard to their taxonomy and classification [4–7]. In other words, the discrimination of morphologically similar species and genera has nowadays become much easier in the context of applying the integrative polyphasic approach.

Throughout this chapter, we present an overview of the key taxonomic characteristics of cyanoprokaryotes and algae. We also present exhaustive insights into the history and modern classification systems, particularly for the blue–green algae. The diverse habitats and global distribution of these intriguing microorganisms have also been our interest and we outline and briefly discuss them across all biomes and also provide some details on the species inhabiting the hot and cool spring habitats.

1.2 Key taxonomic characteristics of cyanoprokaryotes and algae

Algae are a highly heterogeneous group comprising cyanoprokaryotes, characterized by cells mainly lacking membrane-bound organelles, and eukaryotic algae, with cells containing true-shaped organelles [8]. They have representatives in all inland waters and are distributed between eight and 12 major evolutionary lineages [9]. They are classified based on different taxonomic criteria, namely, cell structures (such as plastids, nucleus, composition of cell walls, etc.), physiological characteristics (such as types of pigments, storage products, etc.), or morphological features such as number and position of flagella. The nature of photosynthetic pigments was the primary base for algal classification into different divisions. However, more ultrastructural cellular details, with keystone taxonomic value, have been unveiled with the advent of the electron microscope [8]. For a description of the taxonomic features of the major algal groups treated in this section, we follow and recommend recent phycology texts [9,10]. In general, there is little consensus among taxonomists about the exact number of algal divisions, and the rapidly growing polyphasic approaches are most likely to change our understanding with regard to the classification systems of algae.

The key taxonomic features of the main algal groups in this chapter are summarized in Table 1.1.

Table 1.1

Rewritten and edited after R.G. Sheath, J.D. Wehr, Introduction to the freshwater algae, in: J.D. Wehr, R.G. Sheath, J.P. Kociolek, (Eds.), Freshwater Algae of North America: Ecology and Classification, Academic Press, San Diego, California, 2015, pp. 1–11. D. Sahoo, P. Baweja, General characteristics of algae, in: D. Sahoo, J. Seckbach, (Eds.), The Algae World, Springer, Dordrecht, 2015, pp. 3–29.

1.3 Cyanoprokaryotes: taxonomic classification history, modern age, and perspectives

1.3.1 History of cyanobacterial taxonomy

Cyanobacterial taxonomy has been a challenging field, with numerous criteria being developed and revised in order to attain a system that is stable and consistent. The latter decades of the 19th century were characterized by the documentation of two tribes of blue–green algae, the Coccogoneae (having unicellular reproductive bodies) and Hormogoneae (having few short fragments, like hormogones) [12]. The taxonomy of the Coccogoneae was further elaborated in other works [13]. Interestingly, even before all these developments, Nägeli had documented the unicellular Chroococcaceae already in 1849 [14]. The Hormogoneae tribe was further subjected to more attention in the works of Thuret [12], and Bornet and Flahault [15–20]

Understanding of taxonomy in these early times focused on exploring certain prominent and visible morphological characters. Branching was, amongst others, an important morphological trait that was considered to differentiate filamentous forms of blue–green algae. Broadly speaking, filamentous forms included both the unbranched and branched forms, with the branched forms being further divided into either true branched or false branched forms [21]. The orders Nostocales and Stigonematales were thus recognized in many different systematic studies [22–27]. Another important criterion used for classifying the blue–green algae was the absence or presence of heterocytes, which led to the formation of the families Homocysteae and Heterocysteae in the order Hormogonales. While this system, in the modern times looks satisfactory, it was not accepted by many phycologists in the early years of the 20th century. Prominent proponents of this system were Bornet and Flahault [16–20] and Setchell and Gardner [28]. Elenkin [29] supported this system too, and in fact recognized Heterocysteae and Aheterocysteae, with the latter group having 14 distinct families under the order Oscillatoriales. Thus it is evident that from very early times the presence or absence of different morphological characters intrigued cyanobacterial taxonomists, encouraging them to dive deeper into solving the problems of cyanobacterial classification. During the course of these studies, many new schools of thought emerged, and some of them in the early ages were mentioned above. Moving ahead of the findings of Bornet and Flahault [16–20] and Borzì [30–33], it was Geitler [22–24] who developed a new system of classification in a series of studies and revisions which ultimately led him to recognize four orders: Chroococcales, Dermocarpales, Pleurocapsales, and Hormogonales. At the same time, Frémy [34,35] recognized three orders: Chroococcales, Chamaesiphonales, and Hormogonales. He subdivided the Hormogonales into Homocysteae and Anhomocysteae. This system was also adopted, with some modifications, in the work of Elenkin [29]. Later on Fritsch [25–27], with an enhanced focus on the heterocytous forms, determined the five orders Chroococcales, Chamaesiphonales, Pleurocapsales, Nostocales, and Stigonematales. In 1959 Desikachary [21] broadly accepted Fritsch’s classification, especially in the context of the recognition of the Stigonematales as the most advanced group of cyanobacteria, along with supporting the separation of the Nostocales and Stigonematales. However, differences in the classification of the genera Mastigocladus and Brachytrichia were deviations from the work of Fritsch. Thus even after having differences at the family level of classification of some groups, Desikachary too recognized five orders: Chroococcales, Chamaesiphonales, Pleurocapsales, Nostocales, and Stigonematales. Desikachary’s work also pointed to the importance of physiological, ecological, and cytological features of blue–green algae, which in the coming modern times eventually became part of the accurate taxonomic identification of this prokaryotic algal group. Overall, starting from the late 19th century onwards, the first half of the 20th century witnessed rigorous taxonomic studies from many phycologists all around the globe, which ultimately led to an enhanced basic understanding of the taxonomy and identity of cyanobacteria with a common consensus being centered around unicellular and colonial forms, filamentous nonheterocytous forms, unbranched filamentous heterocytous forms, and branched filamentous heterocytous forms. With the introduction of better planned studies and more clarity on gene markers, in particular during the last four decades, modern taxonomic assessments started to emerge.

1.3.2 The modern age of cyanobacterial taxonomy

The modern age of cyanobacterial taxonomy was characterized by the introduction of more clear and concise descriptions of various taxonomic entities. One of the initial contributions was the work of Prescott [36], who studied all algae, with cyanobacteria constituting a part of his studies. He recognized three main cyanobacterial orders, namely, the Chroococcales, Chamaesiphonales, and Hormogonales, which was basically in agreement with the classification of Frémy [34]. The Hormogonales were subdivided into six families: Oscillatoriaceae, Nostochopsaceae, Stigonemataceae, Rivulariaceae, Scytonemataceae, and Nostocaceae. Another important work of Bourrelly [2] was in congruence with the five order system of Desikachary [21]. Eventually, one of the most well-received and followed contributions came from the work of Rippka et al. [37] in which the cyanobacteria were divided into five sections.

In a study based on 178 strains of cyanobacteria, Rippka et al. [37] aimed to provide stable and consistent generic identities. In total, five sections were proposed, giving recognition to 22 genera. Importantly, this system attempted to identify cyanobacteria in laboratory cultures and took into consideration the morphological changes which were encountered when comparing natural samples with laboratory-grown cultures. Notably, this was also one of the first planned studies attempting to recognize strains on the basis of culture characteristics, rather than the appearance of the samples in nature. Thus the morphological plasticity with change in environmental and culture conditions was addressed in this study. Section I comprised unicellular cells that reproduced by binary fission or budding. Section II also consisted of unicellular cells that reproduced by multiple fissions, leading to the formation of baeocytes. Sections III, IV, and V all contained filamentous cyanobacteria. Section III consisted of taxa not forming heterocytes, akinetes, or hormogonia. Sections IV and V were heterocytous, could form akinetes, and also reproduced by hormogonia formation. Filaments in Section IV divided in only one plane (unbranched), while those in Section V showed division in more than one plane (branched). Interestingly, this system was also an attempt to discuss the bacterial treatment of cyanobacteria rather than following the botanical code, as was done previously by most taxonomists [2,21,22].

After the system of Rippka et al. [37], further progress was made with phylogenetic perspectives being incorporated in the work of Castenholz [38]. This work supported the hypothesis of recognizing small genera [39] as compared to having fewer genera consisting of many species. In this system, emphasis was placed on describing and identifying stable culture characteristics of taxa. Also, in a well-envisioned outlook, the incorporation of more extensive DNA and phylogenetic data was anticipated in future studies. The five orders established in the previous works were referred to as subsections I-V in this system.

1.3.3 Development of the polyphasic approach

The era from 1980 onwards generally saw an increased focus on understanding the genetic characters of cyanobacteria, and taxonomy was not left untouched by these new methods. The better understanding of morphological features and usage of molecular tools (which later extended to phylogenetic methods) resulted in a refreshed focus on issues of cyanobacterial identification and taxonomy. The main methods contributing to these developments were the introduction of electron microscopy and 16 S rRNA gene-based phylogeny. The usage of these strategies helped in the separation of the orders Synechococcales and Chroococcales, the establishment of the separate families of Pseudanabaenaceae and Leptolyngbyaceae, the establishment and better clarity of the entire heterocytous cluster, and the description of numerous new genera and species [40].

Looking closely at the current developments, there are usually two major ways thorough which cyanobacterial taxonomic studies are still progressing. The first school of thought comprises mainly field specialists and ecologists emphasizing the study of natural populations, and hence assigning names usually on the basis of morphological criteria. Genetic studies and phylogenetic interpretations are usually sporadic and do not follow a particular pattern, with no attention being paid to the identification of monophyletic genetic clusters. This approach is clearly informative in terms of discussing a lot of information about the naturally occurring populations, in terms of their morphology and ecology, however, the morphological plasticity and changes that occur in long-term laboratory subculturing are neglected or minimized in most of these studies. Hence, it may eventually result in assigning erroneous, ambiguous, or confusing traits to the taxa being studied. The second pattern of assessment that has come into relevance is the extensive evaluation of isolated laboratory-grown strains that are eventually sequenced and of which the phylogeny is determined. Ultimately, a strain is assigned to a particular cluster, based on its position in the phylogeny. While this second approach clearly defines the traits of laboratory-grown cultures, somehow the naturally occurring samples are not paid equal attention, again resulting in ambiguity in taxonomy [40]. We need to understand that a careful balance is required between both these approaches, and this is where the proper understanding of the polyphasic approach is essential. While it is commonly agreed that this type of balance is necessary, achieving this balance for correct identification is still not universally accepted or understood. Discrete plans of work and methods to establish the identity of particular taxa, in coherence with a polyphasic approach, are hence lacking. But, this level of deviation must be accepted considering the ecological and morphological diversity of cyanobacteria [40]. Also, the use of 16 S rRNA genes as molecular markers is also essential, at least in initial studies, as this gene evolves relatively slowly [40].

Connected to the lack of a consensus scheme in the polyphasic approach, it is equally important to realize the uneven weighting of similar characters in different taxonomic groups. Morphological and ecological characters that may be important in one group of cyanobacteria may not hold much relevance in another group (for example, false branching is important in Scytonema, life cycle events are useful in Nostoc). It must be understood that the differential evolution of these characters may also reflect in phylogenies with higher and better taxon sampling. Thus a universal fit for all sizes mode of understanding cyanobacterial taxonomic issues may never come into existence as these organisms are simply too diverse and complex. Examples of some of these facets include the presence of complicated life cycles in the genus Nostoc, but their absence in the morphologically closely related Nostoc-like genera, such as Aliinostoc or Desikacharya. The presence/absence of gas vesicles is another characteristic that may, or may not, have taxonomic value in different cyanobacterial groups. Due to all these complications, it is desirable to use polyphasic approaches in modern taxonomic schemes, which promotes the combined usage of morphological, ecological, molecular, and phylogenetic methods. Though not fully tested, a broad consensus has been reached in the usage of the polyphasic approach with the genetic criterion being the primary method, and morphological, ecological, and ecophysiological methods being secondary criteria for identifying cyanobacterial taxa. Also, it has been reasonably established that these secondary methods could vary in different groups and lineages [5].

1.3.4 The modern classification of cyanobacteria

With the introduction of modern methods and better understanding of the polyphasic approach, Komárek et al. [4] put forward a modern classification system of cyanobacteria. This was the result of decades of improvements, revisions, and the hard work of many cyanobacterial taxonomists, with Prof. Jiří Komárek leading the way. This was also a result of the completion of the monographic series on cyanobacteria in the Süßwasserflora von Mitteleuropa in which the unicellular, nonheterocytous, and heterocytous cyanobacterial groups were described in detail in three parts [41–43]

The new classification system is based on a few points which need elaboration before discussing the insights of the modern system. The new system basically supports the idea of attaining monophyly at different levels, which could also reflect evolutionary history. Instead of creating larger clusters having a large number of different or unrelated taxa, it is better to have smaller monophyletic entities consisting of related species. The new system keeps the scope open for further revisionary works to attain stability along with well-supported monophyly. It is thus evident that in comparison to the older classification schemes, the new system focuses on phylogenies and the usage of the polyphasic approach. Clarity and consensus are still issues, but the enhanced scope and flexibility of revisions makes the new system of classification much better and comprehensive. It is also important to mention the recommendations of Hoffmann et al. [44,45] that led to the first modern systematic scheme of cyanobacteria in which the class Cyanophyceae was divided into four subclasses: Gloeobacteriophycidae, Synechococcophycidae, Oscillatoriophycidae, and Nostochophycidae. This system differed from all the earlier systems in being based more on phylogeny and modern methods.

The new system of classification also discussed the problematic areas in a more realistic and practical way by reflecting on five broad categories according to the taxonomic clarity/ambiguities present. Accordingly, category I includes all genera which were strongly supported by 16 S rRNA gene phylogeny, and the type species were sequenced. Taxa present in this category are usually strongly supported by polyphasic evaluation and the taxonomy of such genera, at least at present, is more or less stable. Some representatives of this category include Brasilonema, Mojavia, Cyanothece, Cylindrospermum, Microcystis, and Halotia. Category II includes genera whose type species were not studied using molecular methods. Modern methods have been used for evaluating these genera but the ambiguity over the sensu stricto cluster and the positioning of the type species make these genera complicated and challenging. Examples of category II include Aulosira, Hyella, Myxosarcina, Petalonema, and Schizothrix. Category III comprises interesting and complicated larger taxonomic entities like Calothrix, Nostoc, Leptolyngbya, Anabaena, Oscillatoria, Pseudanabaena, Trichormus, and Synechococcus. All these genera are cosmopolitan, traditionally defined, and not monophyletic. These genera usually have a large number of morphotaxa, are often incorrectly identified and have the typical problem of very closely related morphogenera. These genera must be studied further using the polyphasic approach and many revisionary attempts are anticipated in this category. Category IV comprises taxa that lack significant molecular assessment, although they have been described many years ago. The reasons for the lack of molecular data include difficulties in isolation, purification, and cultivation, or sometimes the rare occurrence of many representatives. Some members of this group are doubtful or improperly diagnosed genera. Prominent members of this group are Asterocapsa, Cyanosarcina, Desmosiphon, Lithomyxa, Placoma, and Loriella. Finally, category V is comprised of members which are taxonomically invalid and currently have no nomenclatural standing. Examples include Exococcus, Gervasia, Haplonema, and Lagerheimiella.

The new system of classification mentions the orders Gloeobacterales, Synechococcales, Chroococcales, Spirulinales, Pleurocapsales, Chroococcidiopsidales, Oscillatoriales, and Nostocales (Fig. 1.1). It is notable that the basis of separation at this level of organization was the ultrastructural pattern of thylakoids and preliminary phylogeny. Thus modern taxonomy is clearly a reflection of the evolutionary tendencies of cyanobacteria and supports the idea of genera being monophyletic. It also gives equal weight to understanding the morphological intricacies along with documentation of the habitats and ecological niches. The present system also addresses the issue of cryptogenera (morphologically indistinct, phylogenetically distinct) and the challenges encountered in their description, especially by using the general methods of taxonomic description. Also, morphogenera (differing in morphology, but molecular data insufficient) represent another case study and a challenging taxonomic issue.

Figure 1.1 Phylogenetic positioning of different orders of cyanobacteria inferred by the neighbor joining method based on the 16 S rRNA gene. The evolutionary distances were computed using the Kimura 2-parameter method and are in the units of the number of base substitutions per site. The rate variation among sites was modeled with a gamma distribution (shape parameter=5). The analysis involved 212 nucleotide sequences. Bar, 0.02 changes per nucleotide position. No bootstrap values <50 are shown. Evolutionary analyses were conducted in MEGA5.

Thus the modern taxonomy is indeed a consideration of all the taxonomic reflections that started in the 19th century and are still continuing in the 21st century. In simple terms, this modern system of classification introduces the following aspects that must be tested and also scrutinized by contemporary taxonomists:

1. Usage of the polyphasic approach is essential and it must be applied judiciously as per the taxa under investigation.

2. Molecular and phylogenetic evidences are the primary criteria for establishing taxonomic entities, but they must be accompanied by thorough secondary evidence from morphological and ecological attributes.

3. Cyanobacterial taxonomy will undergo further revisions in the coming decades and there is ample scope for the discovery and creation of more monophyletic generic units.

1.3.5 Present status and the future of cyanobacterial taxonomy

The period after the new classification system implemented was characterized by more clarity and thus enhanced efforts to solve confusing taxonomic issues. This led to the establishment of many new families, genera, and species. The major family level changes included the establishment of the families Oculatellaceae and Trichocoleaceae [46] in the order Synechococcales, the family Aliterellaceae [47] in the order Chroococcidiopsidales, the family Desertifilaceae [48] in the order Oscillatoriales, and the families Calotrichaceae [49], Cyanomargaritaceae [50], Dapisostemonaceae [51], Fortieaceae [4], Geitleriaceae [52], and Heteroscytonemataceae [53] in the order Nostocales. Apart from this, an astonishing number of new genera have also been described (more than 80) since the publication of Komárek et al. [4]. Thus it is evident that the new classification system has indeed shown a way for all modern-day cyanobacterial taxonomists to discover and describe cyanobacterial diversity with continued efforts in an efficient and better directed manner. The near future may entail the introduction of more studies, for instance characterization of the secondary metabolites and unique bioorganic compounds, which could enhance our understanding of cyanobacterial taxonomy. With increased efforts of using genomics-based approaches it is also essential to maintain the nomenclatural rules and most importantly describe the taxa with typification in as much detail as possible [6]. It is advisable to adopt caution while using these modern methods as these methods can sometimes create more confusion due to the absence of proper descriptions and types. This was evident in the study of Walter et al. [54] where genomic analysis resulted into the invalid description of 33 new genera and 28 new species. At present, the careful usage of the polyphasic approach, observance of the nomenclatural rules, and comparative evaluation with all closely related taxa are the way through which cyanobacterial taxonomy can move ahead in a positive direction.

Similar to the cyanophycean taxonomy, the issues of morphological plasticity, the huge amount of heterogeneity, extensive reproductive mechanisms, and complicated life cycles are common characters affecting the taxonomy and systematics of eukaryotic algae. While understanding these features is absolutely essential, synchronizing the evolution of these characters with the modern concepts of polyphasic taxonomy and phylogenetic tools is another aspect that makes the present-day taxonomy of eukaryotic algae a challenging field of study. At present, the modern understanding of green algal systematics divides the Chlorophyceae into two lineages: the Cholorophyta and the Streptophyta. The brown algal systematics has also very recently seen major developments [55] based on 12 molecular markers. The taxonomy and phylogeny of the Phaeophyceae is also complicated, taking into account the presence of life cycle variations in different groups and the complicated process of sexual reproduction. Also, the extensive influence of speciation based on biogeographic patterns is another aspect that makes the taxonomy of Phaeophyceae interesting. Similarly, the current understanding of the taxonomy of red algae is again very complicated as a result of the occurrence of pit connections, pit plugs, and a triphasic life cycle with postfertilization changes. At present the phylum Rhodophyta is divided into two subphylums Rhodophytina and Cyanidiophytina using combined plastid protein sequences [56]. Nonetheless, in spite of the enhanced usage of modern genomic tools and phylogenetic methods, the taxonomy of all eukaryotic algae is still undergoing many revisions and hence just like the cyanophyceae, usage of a polyphasic approach is always recommended for all the eukaryotic algae. The upcoming section on eukaryotic algal taxonomy hence aims to capture the essence of the history of development of well established eukaryotic taxonomic classifications in a nutshell. It must be noted that taxonomy as a branch of science is ever changing and ever challenging, hence it is impossible to discuss in detail the central tenets of eukaryotic algal taxonomy in a single communication.

1.4 History and present-day algal taxonomy

The foundation of modern biological systematics and nomenclature was laid by the Swedish botanist Carl Linnaeus who published the book Species Plantarum in 1753. Linnaeus [57] classified the plant kingdom into 25 classes based on sexual reproduction. He used the term algae for the first time as one of the orders in the class Cryptogamia (plants with hidden reproduction) which included the flowerless plants, but also the genera Conferva, Ulva, Fucus, and Chara, which are now considered algae. Augmentation of our better understanding of the taxonomic classifications of algae, led to the classification of algae into eight and 12 major evolutionary lineages [9].

Classification of algae varies continuously due to the improvement in modern classification techniques resulting in the reclassification and the identification of new species. After the huge efforts exerted by algal taxonomists, starting from the 19th century to date, we simply confirm that the accurate classification of algae has to be conducted based on integrative multifaceted approaches, that is, morphotaxonomy, autecology, molecular studies and DNA fingerprinting, phylogeny, ultrastructure of cell organelles, following life cycle stages, physiological characteristics, and biochemical constituents.

The most acceptable algal classification systems proposed by the algologists are discussed below:

Harvey’s classification[58]: Algae were classified for the first time into four main groups: Chlorospermae (green algae), Melanospermae (brown algae), Rhodospermae (red algae), and Diatomacea (diatoms), based on their pigmentation. In 1843 Kützing published his treatise Phycologia generalis oder Anatomie, Physiologie und Systemkunde der Tange in which 96 families were recognized, 62 families of these were new. This work is of major significance in the history of algal classification.

Eichler’s classification[59]: The author created the new division Thallophyta and classified algae and fungi together in this division. The five-group system of algal classification was proposed on the basis of their color and algae were divided into Cyanophyceae (blue–green algae), Diatomeae (diatoms), Chlorophyceae (green algae), Phaeophyceae (brown algae), and Rhodophyceae (red algae).

Engler and Prantl’s classification[60]: Algae and fungi were grouped together under Euthallophyta and different algal groups were identified, including Schizophyta (blue–green algae), Flagellatae, Dinoflagellata (flagellate protists), diatoms, Chlorophyta (Conjugatae and Chlorophyceae), Charophyta, Phaeophyta, and Rhodophyta.

West’s classification[61]: Algae were divided into four groups on the basis of reproductive structures and presence or absence of flagella: Akontae (flagella absent), Isokontae (flagella of equal size), Heterokontae (flagella of unequal size), and Stephanokontae (flagella crowned).

Pascher’s classification[62]: The first evolutionary scheme of algal classification was proposed based on the phylogeny and relationships among the different algal groups, and algae were classified into eight divisions which were, in turn, subdivided into classes: Cyanophyta, Rhodophyta, Phaeophyta, Chrysophyta, Pyrrophyta, Euglenophyta, Charophyta, and Chlorophyta.

Tilden’s classification[63]: Algae were classified into five groups on the basis of reserve foods, pigmentation, and flagellar structure, number, insertion, and arrangement, namely, Myxophyceae, Rhodophyceae, Phaeophyceae, Chrysophyceae, and Chlorophyceae. According to this system, pigments are of fundamental significance in the development and advancement of algal members, and thus this system supported the retention of algae names based on color.

Fritsch’s classification[64]: The most acceptable and comprehensive algal classification scheme was proposed in this work. Eleven classes were proposed, based on a combination of different characteristics, including the presence or absence of an organized nucleus, photosynthetic pigments, storage products, thallus organization, flagellar arrangement (number and insertion), and reproduction. These classes are Myxophyceae (Cyanophyceae or blue–green algae), Rhodophyceae (red algae), Phaeophyceae (brown algae), Euglenophyceae (euglenoids), Chloromonadineae, Dinophyceae (dinoflagellates), Cryptophyceae, Bacillariophyceae (diatoms), Chrysophyceae (golden-brown or golden algae), Xanthophyceae (yellow-green algae), and Chlorophyceae (green algae).

Smith’s classification[65]: Pascher’s classification system was followed with some modifications. Algae were classified into seven major divisions, each with one or more classes. The seven algal divisions proposed were: Chlorophyta, Euglenophyta, Pyrrophyta, Chrysophyta, Phaeophyta, Cyanophyta, and Rhodophyta.

Papenfuss’s classification[66]: Pascher’s and Fritch’s classification systems were criticized and algae were classified based on their evolutionary relationships. Seven divisions were proposed, namely, Chlorophycophyta, Charophycophyta, Euglenophycophyta, Chrysophycophyta, Pyrrophycophyta, Phaeophycophyta, and Rhodophycophyta, each with one or more classes. He also classified the blue–green algae (Myxophyceae) in a separate phylum, Schizophyta, together with eubacteria.

Chapman’s classification[67]: The four major algal divisions scheme was proposed based on pigmentation, morphological differences, and phylogenetic relationships. Each division was further divided into one or more classes as follows: Myxophycophyta (Myxophyceae), Euphycophyta (Chlorophyceae, Phaeophyceae, and Rhodophyceae), Chrysophycophyta (Chrysophyceae, Xanthophyceae, and Bacillariophyceae) and Pyrrophycophyta (Cryptophyceae and Dinophyceae).

Prescott’s classification[68]: Algae were divided into nine major phyla with different classes based on a combination of taxonomic characters, such as the presence or absence of a true nucleus, photosynthetic pigments, biochemical nature of the cell wall, reserve foods, life history, and reproduction. These phyla were Chlorophyta (Chlorophyceae and Charophyceae), Euglenophyta, Chrysophyta (Bacillariophyceae, Chrysophyceae, and Xanthophyceae), Pyrrophyta (Desmophyceae and Dinophyceae), Phaeophyta (Isogeneratae, Heterogeneratae, and Cyclosporae), Rhodophyta (Bangioideae and Florideae), Cyanophyta (Coccogoneae and Hormogoneae), Cryptophyta, and Chloromonadophyta.

Round’s classification[69]: Algae were divided into two major groups: phylum Cyanophyta in Prokaryota and all other algae in Eukaryota. He classified eukaryotic algae into 11 phyla: Chlorophyta, Charophyta, Euglenophyta, Prasinophyta, Xanthophyta, Haptophyta, Dinophyta, Bacillariophyta, Chrysophyta, Phaeophyta, and Rhodophyta.

Bold and Wynne’s classification[70]: Papenfuss’s classification system was followed and the term phyco- was used before phyta in naming algal divisions. Nine divisions of algae were proposed: Cyanochloronta, Chlorophycophyta, Charophycophyta, Euglenophycophyta, Phaeophycophyta, Chrysophycophyta, Pyrrhophycophyta, Cryptophycophyta, and Rhodophycophyta.s

Parker’s classification[71]: Algae were mainly divided into Prokaryota and Eukaryota on the basis of the presence or absence of membrane-bounded organelles. Prokaryota was further divided into two divisions Cyanophycota (Cyanophyceae) and Prochlorophycota (Prochlorophyceae). Eukaryota included Rhodophycota (Rhodophyceae), Chromophycota (with the classes Chrysophyceae, Prymnesiophyceae, Xanthophyceae, Eustigmatophyceae, Bacillariophyceae, Dinophyceae, Phaeophyceae, Raphidophyceae, and Cryptophyceae), Euglenophycota (Euglenophyceae), and Chlorophyta with three classes, namely, Chlorophyceae, Charophyceae, and Prasinophyceae.

Lee’s classification[8]: This classification system is currently widely accepted. Lee divided algae into two major groups, namely, Prokaryota and Eukaryota, which were further divided into several divisions and classes. Prokaryota only comprised one division, named Cyanophyta with the single class Cyanophyceae. Eukaryota were divided into three main groups, based on structure of the chloroplast envelope membranes:

Group I—algal divisions with chloroplasts surrounded by a double-membraned chloroplast envelope, including Glaucophyta, Rhodophyta, and Chlorophyta.

Group II—algal divisions distinguished by having double-membraned chloroplasts surrounded by one membrane of the chloroplast endoplasmic reticulum. These include Euglenophyta (euglenoids) and Dinophyta (dinoflagellates).

Group III—algal divisions having double-membraned chloroplasts surrounded by two membranes of the chloroplast endoplasmic reticulum envelope. These include Cryptophyta (cryptophytes), Prymnesiophyta (haptophytes), and Heterokontophyta (heterokonts). The latter division was further divided into several classes, including Chrysophyceae, Synurophyceae, Bacillariophyceae, Phaeophyceae, Eustigmatophyceae, Xanthophyceae, and Raphidophyceae. The key taxonomic characteristics for each algal class have been discussed in Section 1.2.

1.5 Global distribution and habitats of cyanoprokaryotes and algae

Algae, including the evolutionarily primitive photoautotrophic cyanoprokaryotes, colonize all three abiotic components of planet Earth, namely, air, land, and water. These organisms are abundant, widely distributed, several are cosmopolitan, and, as long as sunlight and water cooccur, they can occupy all biomes around the globe. Most species are morphologically and physiologically adapted to the specific biotopes in which they live. Although many algae can live in aerial and terrestrial environments, they are by far the most abundant in aquatic habitats.

1.5.1 Aerial (subaerial or aerophytic) algae

Aerial algae inhabit any object in the air, above the soil or may be found on the surface of water. Different types of aerial habitats include exposed bedrock, the soil’s surface, terrestrial bryophytes, tree bark, and anthropogenic structures. Moisture, needed to sustain life, can originate from groundwater seep, precipitation, humidity, or waterfall spray and can be highly variable, ranging from perennially moist to mostly dry [72].

Light, rain, and air humidity are considered to be the most influential factors affecting aerial algae [73], and aerial algal communities are usually adapted to these conditions. Adaptations include mechanisms to retain moisture or limit moisture loss. Some adaptations include a reduction in cell size, morphological changes (especially common in diatoms), as well as mucilage production that aids water retention [74]. As solar radiation is much more intense in aerial habitats, some of these algae produce internal or external protective pigments to protect them against harmful UV-radiation [72].

The terms euaerial and pseudoaerial are often used to distinguish between different types of aerial algae [75]. Algae inhabiting elevated objects, receiving only atmospheric moisture, are termed euaerial, while algae inhabiting areas that receive a fairly constant supply of moisture from seeping groundwater, surface runoff, or waterfall spray are termed pseudoaerial.

On the basis of the habitats and substrates that free-living aerial algae occupy, they can be subdivided into the following types:

• Airborne algae—the presence of airborne algae has long been recognized, since the publication by Ehrenberg [76] in which 18 diatoms in air dust samples, collected by Darwin, were described. Airborne cyanobacteria and algae can be found in sea spray and as minute particles blown around by wind. The most common airborne genera include Gloeocapsa, Chlorella, Chlorococcum, Scenedesmus, Acutodesmus, and Desmodesmus. An extensive review of airborne cyanobacteria and algae, and their health effects, was published by Genitsaris et al. [77]. This review also presented a table in which all airborne cyanobacteria and algal taxa reported by investigators of aerial algae are summarized. A recent study by Saber [78] on the airborne algae of the El-Farafra Oasis (Western Desert of Egypt) revealed five taxa, namely, Myxosarcina chroococcoides (nowadays known as Cyanosarcina chroococcoides), Oscillatoria acuminata (currently Oxynema acuminatum), Lyngbya limnetica (currently regarded as Planktolyngbya limnetica), Schizothrix braunii, and Westiellopsis prolifica. He concluded that the airborne algal propagules were exfoliated from soil surfaces and other aquatic ecosystems into the air.

• Lithophytic (epilythic and endolythic) algae—grow on rocks, stones, bricks, or cement and are commonly found on stone walls, monuments, and walkways. Vaucheria, Nostoc, Gloeocapsa, and many other algae are common genera found on wet rocks. Black spots on stone walls in rainy seasons are often caused by growths of Scytonema. Caves are habitats generally characterized by low light intensities. Pseudoaerial cyanobacteria and algae growing against cave walls and shaded overhangs (Fig. 1.2A–B), receiving moisture from dripping rocks and spray from waterfalls, can also be classified as lithophytic algae, as they represent forms living in the transition zone between aerial and terrestrial (rock) habitats.

• Epixylous algae—grow on dead wood such as poles, posts, and doors.

• Epimetallous algae—grow attached to metal surfaces.

• Epiphytic algae—grow on living plants and are often found in trees. Epiphyllous algae, such as Trentepohlia, grow on the leaves of plants, while epiphloeophytic algae (also known as epiphellous or corticolous algae) are commonly found on bark, stems, or trunks of trees. Algae growing on the bark of trees are often mixed with mosses and liverworts and include several species of cyanobacteria (Aphanothece, Chroococcus, Lyngbya, Phormidium, Porphyrosiphon, Hapalosiphon, Hassalia, Nostoc, Scytonema, and Stigonema), as well as eukaryotic green algae, such as Trentepohlia and Klebsormidium[11]. Epiphytic algae use their hosts for aerial support, but obtain their resources from the atmosphere and because they are excellent examples of commensalism, some aerial epiphytes will be further discussed in Section 1.5.4.

• Epizoic algae—grow on land animals. The most well-known examples are the red alga Rufusia pilicola[80], the cyanobacterium Oscillatoria pilicola[81], and the green alga Trichophilus welckeri[79] found growing in the fur of certain sloth species. There are grooves on the surface of the hair that retain water, allowing the growth of these algae that turn the hair green (Fig. 1.2C–E).

Figure 1.2 Representative habitats of cyanoprokaryotes and algae. (A–B) Aerial (lithophytic) algae, including a population of the heterocytous cyanoprokaryote Petalonema alatum (B), growing against an overhang that receives water from a seepage and dripping rocks, the Drakensberg area, South Africa. (C–E) Hairs of the sloth Choloepus hoffmanni covered with the aerial (epizoic) green Trichophilus-like alga. (D–E) Close-up views showing details of the Trichophilus-like alga [79]. (F) Terrestrial (cryptophytic) cyanobacteria growing just below the surface of the soil. (G) The pennate diatom Surirella sp. acting as a substrate for the epiphytic green alga Characium sp. (H–I) Pool in the Kruger National Park, South Africa, discolored red due to Euglena sanguinea blooms. E. sanguinea single cell (Fig. I) with red astaxanthin pigments and white paramylon granules. (J–K) Floating masses of Spirogyra sp. and Zygnema sp. in an urban lentic pond in Potchefstroom, South Africa. (L–M) Bloom of the saxitoxins-producing cyanobacterium Dolichospermum circinale in the Fitzroy River Barrage, Central Queensland, Australia. (M) Close-up view of D. circinale trichomes depicting akinetes and heterocytes. Scale bars=20 µm. Source: (A–B) Anatoliy Levanets. (D–E) From M. Suutari, M. Majaneva, D.P. Fewer, B. Voirin, A. Aiello, T. Friedl, et al., Molecular evidence for a diverse green algal community growing in the hair of sloths and a specific association with Trichophilus welckeri (Chlorophyta, Ulvophyceae), BMC Evol. Biol. 10 (1) (2010) 86–97. (F) S. Janse van Vuuren. (G) Jonathan Taylor. (H–I) J. Taylor and Marno Laubscher. (J–K) S. Janse van Vuuren. (L–M) Glenn McGregor.

1.5.2 Terrestrial algae

Cyanobacteria and eukaryotic algae occur in every terrestrial habitat on our planet. Terrestrial algae can occur on the surface of the soil or at depths upto several centimeters in the soil or in/on soil crusts (Fig. 1.2F). Similar to aerial algae, it is well-established that solar radiation, water, and temperature are the most important abiotic factors governing the distribution, metabolism, and life history strategies of terrestrial algae [82].

The algal flora of the soil includes members of the Cyanophyta, Chlorophyta, Euglenophyta, Chrysophyta, and Rhodophyta [82]. Cyanobacteria and eukaryotic green algae are usually the most common taxa in terrestrial environments. Green algal genera commonly encountered in soils are Chlamydomonas, Chlorella, Chlorococcum, and Tetracystis [1], whilst common cyanobacteria include Anabaena, Gloeocapsa, Microcoleus, Nostoc, Phormidium, Westiellopsis, and Scytonema [83,84]. A study by Saber et al. [85] on Egyptian hyperarid desert habitats unveiled four interesting green algal isolates, based on morphological and molecular evidence, and one of them was a genus and species new to science described as Pharao desertorum. In general, the biodiversity of soil algae is still grossly understudied, and there are likely still many interesting species to be described using combined polyphasic approaches.

Different authors have different viewpoints about the classification of terrestrial algae. Petersen [75] defined three major categories based on their habitats, namely:

• Aeroterrestrial algae—occurring on substrates that are elevated above the ground.

• Hydroterrestrial algae—growing on permanently wet soil.

• Euterrestrial algae—including both epiterranean and subterranean forms. Tiffany [86] used the term edaphophytic (soil) algae for these algae and subdivided them into:

– Saphophytic algae, representing surface forms. Examples include many species of cyanobacteria found upon the surface of the soil. Besides these, Botrydium, Fritschiella, Mesotaenium, Oedocladium, Protosiphon, Vaucheria, and many other algae, grow on the surface of wet soils.

– Cryptophytic algae, representing subsurface forms. Anabaena, Calothrix, Cylindrospermum, Nodularia, Scytonema, Stigonema, and Trichormus have been reported from rice paddy fields, where heterocytous forms fix atmospheric nitrogen in the soil.

Some terrestrial habitats are extremely hostile environments, ranging from very arid areas, rocks in hot and cold deserts, Antarctic soils, and highly acidic postmining sites. Extreme fluctuations in environmental conditions, such as aridity and/or low or high levels of temperature or light intensity, can result in stress, leading to morphological and physiological adaptations. Cyanobacteria produce mucilage, thick sheaths, or protective pigments as adaptations [83]. The green alga Zygogonium forms thick mats with extremely high water-holding capacity [87], and the species Zygogonium ericetorum produces reduced cytoplasm, thicker walls, and solutes with UV-absorbing capacities [88]. Several green algal taxa can survive extended periods without moisture, after which they are able to recover upon receiving moisture. Friedmann et al. [89] classified the desert soil algae into five categories:

• Endedaphic algae—living in the desert soils.

• Epidaphic algae—living on the surface of desert soils.

• Hypolithic algae—living on the lower surface of stones on desert soils.

• Chasmolithic algae—living in the rock fissures in desert soils.

• Endolithic algae—penetrate rocks as they grow.

A variety of algae can also live in symbiosis with terrestrial plants. These symbiotic terrestrial algae are discussed, together with aerial and aquatic symbiotic algae, in Section 1.5.4.

1.5.3 Aquatic algae

The majority of algae are aquatic, yet the word aquatic is almost limited and restricted in its ability to encompass the diversity and complexity of these habitats. A multitude of habitats can be distinguished, depending on the classification system used.

Classification of habitats can be based on the position where the cyanobacteria or algae live in the water body (e.g., zone in the sea, lake, dam, river, or pond), the way that they live (epiphytic, epizoic, symbiotic, parasitic, etc.), or how they maintain their position in the water column (e.g., planktonic vs. benthic algae).

In both marine and freshwater habitats epiphytic algae are found living upon other species of algae (Fig. 1.2G). Larger algal forms, such as Cladophora, Chara, or Nitella, may serve as substrata for epiphytic diatoms and other algae, such as Coleochaete nitellarum [1]. Chaetonema is found to be epiphytic on the mucilaginous masses of Tetraspora and Batrachospermum [11]. In the marine environment more than 50 epiphytic algal species have been reported growing on the stipes and holdfasts of Ecklonia maxima (sea bamboo—a species of kelp [90]). Species of Carpoblepharis, Polysiphonia virgate, and Suhria vittata have been identified as the most important kelp epiphytes [91]. Several algae, of which some are mentioned in Section 1.5.4, can also live as epiphytes on aquatic plants. Species of Coleochaete are, for instance, epiphytic on Ipomoea, Typha, Vallisneria, and several other aquatic plants. Rivularia species are commonly found as epiphytes on Potamogeton pectinatus [92].

Epizoic algae include a large amount of species living on aquatic animals such as turtles, snails, shellfish, and fish, both in marine and freshwater environments. Basicladia, Dermatophyton, Oscillatoria, and Protoderma are attached to the backs of turtles [11]. Kanjer et al. [93] studied the diatom community structure on the skin of loggerhead sea turtle heads and 113 highly specialized diatom taxa were recorded. Out of these taxa, the probably obligate epizoic diatoms Achnanthes elongata, Chelonicola sp., and Poulinea lepidochelicola contributed upto 97.1% of the total diatom abundance. Several members of the Ulotrichales (Microspora, Ulothrix, Uronema), Cladophorales (Cladophora and Rhizoclonium), Chaetophorales (Chaetophora, Coleochaeta, and Stigeoclonium), and Oedogoniales (Oedogonium spp.) grow upon mollusk shells [11]. Rhopalosolen saccatus was observed growing on at least two cladocerans (Daphnia similis and Simocephalus vetulus) by Holland and Hergenrader [94] while Characium and Characiopsis occur on the legs of Branchipus (fairy shrimp [95]) as well as on Anopheles larvae [96]. Stigeoclonium is epizoic on the gills of fish [95].

Endophytic and endozoic algae are symbiotic and live in close association with other algae, plants and animals (Section 1.5.4), while parasitic algae (discussed in Section 1.5.5) may exploit their hosts to survive.

The majority of aquatic algae are, however, free-living and they can live in a wide range of salinities, ranging from freshwater, brackish water, marine water, to halophilic environments, characterized by extremely high salt concentrations. In this section two major habitats of free-living aquatic algae will be discussed, namely, marine and freshwater habitats, while halophilic environments and halophilic algae will be discussed in Section 1.5.6, as part of extreme environments.

• Marine and salt water habitats—they live in many different habitats within the sediment of intertidal areas, as well as in the open water of oceans. These habitats include:

– Estuaries—besides being planktonic, algae also inhabit the top millimeters of sediment where they live interstitially between the sediment grains enabling them to conduct photosynthesis.

– Sand flats and saltmarshes—in these areas algae can be benthic (living in or on the bottom, often attached to a substrate) or planktonic (free-floating), and in both cases the assemblage is often dominated by diatoms.

– Muddy shores—large quantities of various cyanoprokaryotes and algae such as diatoms, dinoflagellates, and filamentous green and brown algae live interstitially within sediment particles.

– Bare soft substrates—soft substrates are defined as all areas of nonvegetated fine-sediment bottom occurring within estuarine and marine waters below low tide level. Examples of soft substrates include mud, ooze, silt, sand, shell grit, and finer gravels.

– Oceans—in the ocean most marine algae live in the subtidal zone while other species can be found in the splash zone. The open water of oceans is mostly dominated by planktonic algae.

– As a rule, red algae (Rhodophyta), dinoflagellates (Dinophyta), and brown algae (Phaeophyceae) are generally more diverse in marine than in fresh waters [1].

• Freshwater habitats—these habitats are diverse and differ considerably between different types of waterbodies. Epilithic habitats in the freshwater environment include submersed stones, boulders, and bedrock to which a variety of algae can attach. Algal taxa such as Chamaesiphon spp., Gongrosira incrustans, Heribaudiella fluviatilis, Rivularia spp., and Tolypothrix distorta, occurring in stony streams, are commonly reported from epilithic habitats [97]. Epipelic habitats are home to a variety of benthic algae colonizing sediments and mud, whilst epipsammic habitats consist of a layer of sand to which benthic algae attach. The abovementioned habitats can be found in both standing (lentic) and flowing (lotic) waters.

– Lentic water bodies—lentic water bodies consist of stagnant (or extremely slow flowing) water and include ditches, seeps, lakes, reservoirs (dams), ponds, pools, wetlands, swamps, and marshes. The size of lentic waterbodies may range extensively, from extremely small rainwater pools to larger lakes, reservoirs, or dams (man-made structures), to extremely large natural lakes such as Lake Baikal or Tanganyika. Small pools and ponds may have distinctive algal assemblages, as the surrounding land use may influence the composition of the algal assemblage [1]. Bright red blooms by some Euglena species, for example, E. sanguinea, a toxic species, are often observed in ponds from which animals drink, wetlands, waterholes on golf courses, and sewage lagoons [98]. The red discoloration of the water is the result of a mixture of carotenoid pigments (astaxanthin being the most abundant) inside the algae. E. sanguinea has recently formed extensive blooms in small ponds from which animals drink in the Kruger National Park, South Africa [99] (Fig. 1.2H–I). Other algal genera commonly encountered in small stagnant pools or ponds, include Chlamydomonas, Desmodesmus, Hydrodictyon, Pediastrum, Scenedesmus, Spirogyra, Volvox, and Zygnema (Fig. 1.2J–K).

In larger, deep lentic water bodies, such as lakes, dams, and reservoirs, at least four major zones have been identified, in which different algal assemblages may occur:

1. Littoral zone—this is near the shore of the lake, it is usually shallow, so that sunlight can penetrate all the way to the sediments, allowing an abundance of aquatic plants (macrophytes) and algal growth. Cyanobacteria and algae are often intermingled with macrophytes that provide a sheltered environment. Many vertebrates (waterbirds, mammals), invertebrates (e.g., insects, zooplankton), snails and fish also live in the littoral zone, feeding on algae living in the stable environment between the macrophytes. The littoral zone is home to a variety of algae, including amongst others a mixture of (pseudo) planktonic (free floating) forms, benthic (attached) species, symbiotic and parasitic species.

2. Pelagic (limnetic) zone—this is the open water area of the lake/reservoir where light does not penetrate to the bottom. The pelagic zone can be subdivided into the euphotic zone or epilimnion (zone in which light penetrates, down to the depth where photosynthetic active radiation reaches 1% of radiation incident on the water surface) and the profundal zone or hypolimnion (no light penetration). Rooted plants cannot grow in the pelagic zone as it is generally too deep for roots to reach the bottom. Microalgae in the euphotic zone, are mostly dominated by planktonic forms (phytoplankton), exhibiting different adaptations to avoid sinking. Numerous algae (neuston) can also attach to the surface of the air/water interface where they keep their position by means of the surface tension.

3. Profundal zone—this zone represents the deepwater layers of the hypolimnion below the euphotic zone. The profundal zone is usually dark in deep lakes as sunlight does not penetrate to such a depth. Photosynthetic algae are typically absent (though some algae can switch to heterotrophic metabolism to temporarily survive in dark conditions) and heterotrophic forms dominate this layer.

Several authors identified depth-distribution zones while analyzing the spatial structure of algal assemblages along littoral depth gradients (e.g., Cantonati et al. [100] for diatoms; Cantonati et al. [101] for soft algae and cyanoprokaryotes). Most frequently three depth distribution zones were identified and named: shallow, mid-depth, and deep. Generally, some disturbance factor is found to be most determinant in the shallow zone, whilst the mid-depth and deep zones are stable, with the latter being affected by extreme light reduction. In a classic paper, Kann and Sauer [102] described a remarkable periphyton of different colorings composed of pigmented algae typically found in the deeper part of lakes ("Rotbunte Tiefenbiocönose").

– Lotic water bodies: In contrast to lentic water bodies, lotic water bodies consist of flowing water, such as those in creeks, brooks, springs, streams, and rivers, and it may harbor different types of algal assemblages than those found in standing waters. In general, lotic bodies may include a combination of different types of habitats, depending on the flow rate of the water. If the water is slow-flowing in particular areas of, for examle, small streams or large rivers, it can mimic lentic habitats and similar algal assemblages may be found.

Groundwater-dependent habitats, such as fountains, springs, and drilled wells, are important freshwater sources and some may represent extreme habitats (e.g., thermal-to-hot and acidic springs; see Section 1.5.6), sustaining unique algal assemblages.

1. Spring habitats—springs are keystone ecosystems that are rapidly getting impaired and disappearing because of unchecked appropriation of groundwater and site-specific habitat destruction [103]. Since springs are ecotones (i.e., transitional environments) linking groundwater and surface water systems [104], their study requires the integration of multiple disciplines, particularly ecology and hydrogeology [105]. Springs harbor a disproportionately high gamma-biodiversity [106] due to their intrasite substrate heterogeneity and intersite diversity of habitat conditions, as related to extensive variation in their geological age and aquifer geochemistry, and to their widespread distribution across many climatic zones, geological provinces, and biogeographic regions [104] Although some (e.g., geothermal) springs are inhospitable and colonized only by specialized, extremophilic microbial species (these will be discussed in Section 1.5.6), other springs contain multiple microhabitats and consequently diverse assemblages of microbial, plant, and animal life [103,104]. According to Cantonati et al. [107,108], the most common and characteristic algae and cyanoprokaryotes of major spring types are as follows. Iron springs have low pH, high iron and sulfates, and host a few species of filamentous chlorophytes and xanthophytes (Tribonema spp.), plus abundant growth of iron bacteria; diatoms are typically represented by species-poor assemblages with low numbers of individuals. Seepages and pool springs have low current flow, fine-particle-size substrata, and mostly slightly acidic pH; cyanobacteria are often lacking, and filamentous chlorophytes (Spirogyra spp., Mougeotia spp., Microspora spp.) dominate; diatom communities are characterized by the mire-species, such as Frustulia crassinervia, acidophilous taxa, such as Tabellaria flocculosa, very low-alkalinity indicators, such as Psammothidium acidoclinatum, and many Eunotia species (e.g., E. borealpina, E. exigua, E. tenella). Flowing springs on siliceous substratum are often located at higher elevations, with low to very low conductivities, and frequently with higher discharge; the benthic algae are dominated by rheophilic cyanobacteria, and by the rheobiontic chrysophyte Hydrurus foetidus; the cyanobacterium Tapinothrix janthina is also common whilst in the carbonate flowing springs it was replaced by Tapinothrix varians; common diatoms are Odontidium mesodon, O. hyemale, Eunotia minor, Navicula exilis, and Planothidium lanceolatum. Mid- to high-altitude, oligotrophic, carbonate flowing springs with medium conductivities and/or affected by seasonal desiccation host benthic-algae assemblages dominated by cyanobacteria (Chroococcales and Oscillatoriales including the rheophilic T. varians); common diatoms are Achnanthidium pyrenaicum, A. lineare, A. pfisteri, Gomphonema elegantissimum, Nitzschia fonticola, Humidophila perpusilla, H. contenta, Planothidium frequentissimum, Meridion circulare, and Achnanthidium dolomiticum. Low-altitude, mostly shaded and nitrate-enriched carbonate rheocrenes, with medium–high conductivities include mainly cyanobacteria (Pleurocapsa minor, the eutraphentic Phormidium retzii), and red algae (Audouinella spp., Hildenbrandia rivularis); diatoms include Cocconeis euglypta, C. lineata, C. pseudolineata, Amphora pediculus, A. inariensis, Caloneis fontinalis, Reimeria spp., and Eunotia arcubus. Hygropetric rheocrenes, with mid-high conductivities and low to moderate current flow, are characterized mainly by cyanobacteria (Rivularia spp. and Plectonema tomasinianum but also Ammatoidea normanni, and the pseudaerial Calothrix parietina); diatoms include Encyonopsis microcephala, E. cesatii, Gomphonema lateripunctatum, Delicatophycus delicatulus, D. minutus, Denticula tenuis, and Cymbopleura austriaca. The most widespread benthic algae in limestone-precipitating springs [109], located at low altitudes and with high conductivities, are the desmid Oocardium stratum, the cyanoprokaryotes Phormidium incrustatum and Tapinothrix crustacea; other characteristic cyanobacteria belong to the genera Scytonema, Dichothrix, Schizothrix, Gloeocapsopsis, and Gloeothece; diatoms include Achnanthidium trinode, Brachysira calcicola, Denticula elegans, and Cymbella diminuta.

2. Stream and river habitats—planktonic algae are common in large rivers (in streams there may be algal drift) as they are kept in suspension by the continuous mixing of the flowing water (Fig. 1.2L–M). However, streams and rivers represent complex habitats harboring a variety of other microhabitats, such as those sheltered by large boulders and stones. Cyanobacteria and algae living in these sheltered microhabitats may resemble those found in lentic systems. Sheltered microhabitats inside slow-flowing water may also be the home of various benthic species, for example, Chara, Chamaesiphon, and Cladophora, growing attached to substrates in the water. Small microscopic algae, for instance the diatom Gomphonema, may also attach to substrates (stones or boulders in the riverbed) by mucilage stalks (Fig. 1.3A–B). In sheltered patches, filamentous algae may also occur where they act as substrates for a variety of other epiphytic algal species.

Streams and rivers may also consist of stretches of slow-flowing water, alternating with areas marked by rapid and fast-flowing patches of water. Large filamentous algae, such as Enteromorpha (currently moved taxonomically to Ulva) and Vaucheria, are generally found in slow-flowing water, while fast-flowing water is often characterized by fluviatile algae, such as Ulothrix, which is common in mountain falls [110]. Genera such as Stigeoclonium, Batrachospermum and Lemanea were also reported from several swift running streams [111]. Cladophora glomerata is very common in flowing water, for example, the Nile River, where it is often responsible for nuisance conditions. Filaments of Cladophoraglomerata are particularly abundant in concrete-lined canal systems, for example, irrigation canals (Fig. 1.3C–D), or water features such as fountains (Fig. 1.3E–F). At a young stage the filaments are anchored to the concrete by means of rhizoids, but as they mature they will detach, becoming free-floating.

Figure 1.3 Representative habitats of cyanoprokaryotes and algae. (A) Stones covered with growths of freshwater, benthic diatoms in a stream bed. (B) Gomphonema truncatum var. turgidum, a pennate diatom, attached to the substrate by mucilage stalks. (C–D) Cladophora glomerata filaments causing nuisance conditions in irrigation channels. (E–F) C. glomerata filaments growing against the concrete lining of a water feature in front of the main building of the North-West University, Potchefstroom, South Africa. (G–H) Stones covered with crustose and foliose lichens (symbiosis between algae or cyanobacteria and fungi) in the botanical garden of the North-West University, Potchefstroom. (I) Stem of a tree where the bark is covered with various lichens. (J) Mass development of Azolla filliculoides (harboring the symbiotic nitrogen-fixing Trichormus azollae, Fig. K) in a roadside pond between Frankfort and Heilbron, South Africa. Scale bars=20 µm. Source: (A) S. Janse van Vuuren. (B) J. Taylor. (C–D) K. du Plessis. (E–H) S. Janse van Vuuren. (I) A.A. Saber. (J) S. Janse van Vuuren. (K) S. Janse van Vuuren and J. Taylor.

1.5.4 Symbiotic algae

Symbiotic algae are widespread and common and may be found in all three of the abovementioned habitats (aerial, terrestrial, and aquatic), where they live in symbiotic relationships with a variety of organisms, including plants, animals such as ciliates, sponges, and mollusks, as well as fungi. In these symbiotic relationships, the cyanobacteria or algae supply organic substances, derived from photosynthesis to the host organism which, in turn, provides protection to the algal cells.

The most striking example of symbiosis in aerial environments is in the form of lichens (Fig. 1.3G–I), where cyanobacteria or algae live in symbiotic associations with fungi. Various cyanobacteria genera, for example, Chroococcus, Gloeocapsa, Microcystis, Nostoc, and Scytonema, have been isolated from lichens [110]. Chlorella, Coccomyxa, Palmella, and Protococcus are green algal symbionts also found in lichens [110]. The most common alga in terrestrial lichens is a unicellular green alga belonging to the genus Trebouxia [112].

In terrestrial environments there are numerous examples of cyanobacteria and algae that live in symbiosis with plants or animals. A few examples are listed below:

• Endophytic algae—cyanobacteria or algae living inside the tissue of plants.

– Nostoc lives in symbiosis with thalloid liverworts (Blasia pusilla and Cavicularia densa) and all hornworts (e.g., Anthoceros, Notothylas, and Phaeoceros spp.), where the Nostoc colonies fix nitrogen for their hosts. Nostoc can also be found in the leaves of a variety of terrestrial bryophytes (feather mosses and Sphagnum), ferns, cycads, and wetland plants such as Gunnera.

– Nostoc cycadae is found in the coralloid roots of the cycad, Cycas.

– Filamentous cyanobacteria were also found inside the land plant, Aglaophyton major.

• Endozoic algae—cyanobacteria or algae that live inside the body of animals.

– There are about 14 species in the family Oscillatoriaceae found in the digestive and respiratory tracts of various vertebrates [110,113]. However, it seems as if endozoic algae are much less common in terrestrial environments compared to aquatic environments.

– Anabaeniolum lives in unicellular animals and it was also found living in the digestive tract of mammals, including man [113].

Aquatic environments (both marine and freshwater) are characterized by many symbiotic relationships between cyanobacteria or algae on the one hand, and aquatic plants or animals on the other hand. Examples are listed below:

• Lichens—although Trebouxia is the most common algal genus in terrestrial lichens, it is rarely a phytobiont in aquatic lichens [114]. The cyanobacteria Calothrix (in Lichina), Nostoc (in Pyrenocollema), Stigonema (in Ephebe), and the green algae Stichococcus (in Staurothele), and Dilabifilum and Coccobotrys (in Verrucaria) are common in aquatic lichens [114]. Heterococcus