Analysis of molecular diversity within single cyanobacterial colonies from environmental samples.

Attached or floating macroscopic cyanobacteria can be found in shallow waters and can be easily hand-collected, but their identification is often challenging due to their high morphological variability. In addition, many members of environmental samples lose their morphological adaptations under controlled conditions, making the integration of analyses of field populations and derived isolated cultures necessary in order to evaluate phenotypic plasticity for identification purposes. Therefore, in this study, twenty-nine macroscopic field samples were analyzed by Illumina sequencing and parallel optical microscopy. Some colonies showed the typical morphological characteristics of Rivularia biasolettiana, and others showed those of Rivularia haematites. However, other Rivularia-like colonies showed ambiguous morphologies, and some of them showed the phenotypic features of the new genus Cyanomargarita, which is virtually indistinguishable from Rivularia in the field. In all of the colonies, phylotype composition was highly heterogeneous, with abundances varying depending on the analyzed sample. Some colonies were dominated (97-99%) by a single phylotype, while in others, the percentage of the dominant phylotype decreased to approximately 50-60%. Surprisingly, the same dominant phylotype was found in R. biasolettiana and R. haematites colonies. The relationships between environmental and/or biological factors and morphological variability in these colonies are discussed.

Introduction

Cyanobacteria are a very special group of gram-negative prokaryotes. Because they developed the ability to use water as an electron donor inpan> oxygenic photosynpan>thesis, approximately 3.6 billion years ago[1], they played an important role inpan> the evolution of life on Earth, the subsequent generation of molecular O2, and the oxygenation of the atmosphere[2]. Cyanobacteria are also the ancestors of chloroplasts[3,4]. In addition, many cyanobacteria are capable of fixing atmospheric N2 and thus play an important role in nitrogen cycling[5].

It is easy to understand why cyanobacteria were previously called blue-green algae sinpan>ce, inpan> addition to performinpan>g plant-like oxygenic photosynpan>thesis, macroscopic green forms similar to algae can be easily found and observed by the naked eye, with a cosmopolitan distribution ranging from hot hyperarid deserts to polar aquatic environments[6]. These alga-like forms, in which individuals are microscopic but exhibit macroscopic growth, have been described as colonies, thalli, mats, tufts, thin coatings, soft gelatinous covers, subspherical globes, tightly attached felts, etc.[7-9].

The importance of characterizing and identifying natural cyanobacterial populations in order to compare them with corresponding cultures, which are further used, e.g., in phylogenetic analysis or potential applications in biotechnology, has been emphasized[10-13]. However, unfortunately, the majority of recent studies were based only on isolated strains and morphological descriptions corresponding to culture media, and controlled conditions were often different from the characteristics found in the environments where highly diverse cyanobacteria live[7,13]. In a previous study, we compared phenotypic characteristics of natural populations and isolated cultures from n class="Species">environmental samples and found large differences between them, which can lead to misidentification of strainpan>s[12].

Rivulariaceae includes all the heterocystous cyanobacteria with tapered trichomes, with a clear distinction from the base to the apex. A terminal heterocyst (heterocyte) occurs at the broad basal end of the trichomes, and a sheath encloses everything but the heterocyst[7]. These tapering cyanobacteria include many visually conspicuous morphotypes found widely in different aquatic environments; for instance, Rivularia, Dichothrix and Gloeotrichia form macroscopic attached or floating colonies in shallow waters, and many species of n class="Species">Calothrix also form a macroscopic thallus with a characteristic appearance[14].

Rivularia colonies are hemispherical or almost spherical, with more or less parallel sheathed trichomes arranged radially inside colonies; the trichomes often have false branches. Dichothrix forms small colonies of various shapes, mostly cushions or dense tufts; the trichomes are subdichotomic and falsely branched, and there are often many trichomes inside one sheath. n class="Species">Calothrix inpan>cludes all the forms growinpan>g as inpan>dividual filaments or ill-definpan>ed colonies. Filaments inpan> Gloeotrichia colonies are easy to distinpan>guish by their ability to form pan> class="Disease">akinetes[7,14].

Recently, a new genus of tapering heterocystous cyanobacteria, Cyanomargarita, was described[15]. Natural populations were completely consistent with the description of Rivularia; however, upon sequencinpan>g, they were found to be phylogenetically distant from Rivularia. In addition, several other new genera of taperinpan>g cyanobacteria have been described, such as Macrochaete[16] and Dulcicalothrix[17], but these were based only on isolated cultured strains; therefore, the characteristics of natural populations are unknown.

Nevertheless, assessments of conspicuous natural populations have suggested the heterogeneity of colonies[14]. A previous analysis indicated that Rivularia colonies were heterogeneous, where three different morphological types of tapering trichomes were isolated from a single colony of Rivularia[18], and our previous studies combining morphological characterization and genetic characterization via 16S rRNA and phycocyanin operon genes in Rivularia colonies suggested genotypic diversity within a single colony[11].

To study the variability and proportions of genotypes within single colonies, 28 Rivularia-like colonies were collected and analyzed by Illumina sequencing (16S rRNA gene) and parallel optical microscopy. In addition, other type of macroscopic growth not showing the typical hemispherical shape of Rivularia colonies but rather a brush-like Dichothrix tuft was also assessed for comparison with other Rivulariaceae.

Since the occurrence of Rivularia colonies is related to oligotrophic, high-altitude mountain areas and/or clean calcareous running waters[14], where they carry out activities such as n class="Chemical">N2 fixation[19] and phosphatase activity[20] inpan> response to the low levels of combinpan>ed N and P, respectively, different oligotrophic systems, with previously studied Rivularia colonies[11,19-23], inpan> a latitudinpan>al gradient inpan> Spainpan>, were selected. In addition, another location inpan> northernpan> Enpan>gland, where Rivularia colonies have long occurred and been analyzed[24-26] was chosen to assess possible geographic variations.

Results

Morphological characterization of environmental samples

Twenty-eight collected samples (Table 1) showed a macroscopic Rivularia-like morphology in which hemispherical or slightly irregular- hemispherical lobate colonies approximately 0.5–3 cm in diameter/length could be observed (Figs. 1, 2, 3, 4 and 5). After microscopic evaluation, the Rivularia-like colonies could be separated according to their specific features.

Table 1

Macroscopic environmental samples analyzed in this study.

Environmental sample	Geographical origin
MUD1 tuft	Muga River, Pyrenees, Girona, north-east Spain
MU4 colony	Muga River, Pyrenees, Girona, north-east Spain
MU5 colony	Muga River, Pyrenees, Girona, north-east Spain
GG1 colony	Guarga River, Pre-Pyrenees, Huesca, north-east Spain
GG2 colony	Guarga River, Pre-Pyrenees, Huesca, north-east Spain
OSI3 colony	Osia River, Pyrenees, Huesca, north-east Spain
ARA4 colony	Aras River, Pyrenees, Huesca, north-east Spain
GDL1 colony	Guadiela River, Hoz de Beteta, Cuenca, central Spain
GOR1 colony	Gordale Beck, West Yorkshire, northern England, UK
GOR2 colony	Gordale Beck, West Yorkshire, northern England, UK
GOR3 colony	Gordale Beck, West Yorkshire, northern England, UK
GOR4 colony	Gordale Beck, West Yorkshire, northern England, UK
GOR5 colony	Gordale Beck, West Yorkshire, northern England, UK
GOR11 colony	Gordale Beck, West Yorkshire, northern England, UK
GOR12 colony	Gordale Beck, West Yorkshire, northern England, UK
HOY3 colony	Hoyas stream, Paterna del Madera, Albacete, south-east Spain
HOY5 colony	Hoyas stream, Paterna del Madera, Albacete, south-east Spain
HOY14 colony	Hoyas stream, Paterna del Madera, Albacete, south-east Spain
BAT2 colony	Bogarra River, Batán de Bogarra, Albacete, south-east Spain
BAT4 colony	Bogarra River, Batán de Bogarra, Albacete, south-east Spain
BAT5 colony	Bogarra River, Batán de Bogarra, Albacete, south-east Spain
BAT12 colony	Bogarra River, Batán de Bogarra, Albacete, south-east Spain
BAT13 colony	Bogarra River, Batán de Bogarra, Albacete, south-east Spain
BAT14 colony	Bogarra River, Batán de Bogarra, Albacete, south-east Spain
END1 colony	Endrinales stream, Espineras, Albacete, south-east Spain
END2 colony	Endrinales stream, Espineras, Albacete, south-east Spain
END5 colony	Endrinales stream, Espineras, Albacete, south-east Spain
END8 colony	Endrinales stream, Espineras, Albacete, south-east Spain
END15 colony	Endrinales stream, Espineras, Albacete, south-east Spain

Figure 1

Photographs and light micrographs of Rivularia biasolettiana-type colonies. (a) BAT5 and (b) BAT14 colonies from the Bogarra River. (c) GG2 colony from the Guarga River. (d) Radial arrangement of filaments in the BAT5 colony from the Bogarra River. (e) Detail of the radial arrangement of filaments in the END5 colony from the Endrinales River. (f) and (g) BAT12 filaments showing pigmented or hyaline sheaths. (h) Hairs in filaments of the GG2 colony from the Guarga River. (i) Meristematic zones showing divided trichomes persisting within common old sheaths in END5 from the Endrinales River. Bars 1 mm (a,b), 200 μm (d), 100 μm (e), 20 μm (f–i).

Figure 2

Light micrographs of Rivularia haematites-type colonies. (a) HOY14 and (b) HOY13 colonies from the Hoyas stream, showing high calcification and concentric zonation. Sections of END15 (c) and END2 (d) colonies from the Endrinales stream, showing zonation after decalcification with EDTA corresponding to layers of calcite, still obvious due to differences in sheath density and scytonemin pigmentation. Parallel and densely arranged filaments in the GOR4 (e) and GOR5 (f) colonies from Gordale Beck. (g) Hairs of trichomes of the HOY3 colony from the Hoyas stream. (h) New trichomes persisting within common old sheaths in the END15 colony from the Endrinales stream. Bars 1 mm (a,b), 200 μm (c), 100 μm (d), 20 μm (e–h).

Figure 3

Light micrographs of Cyanomargarita colonies. (a) Hemispherical END1 colony from the Endrinales stream. (b) Section of the END1 colony showing zonation. (c) Radial arrangement of filaments in the ARA4 colony from the Aras River. (d) Layers with distinct pigmentation in the decalcified END8 colony from the Endrinales stream. (e) Tapering trichomes in the END8 colony from the Endrinales stream, similar to those of Rivularia. (f) Parallel and densely arranged filaments in the END1 colony from the Endrinales stream. Colored and lamellated sheaths of filaments in the ARA4 colony from the Aras River and (g) hyaline sheaths in other parts of the same ARA4 colony (h). Bars 1 mm (a,b), 200 μm (c,d), 100 μm (e,f), 20 μm (g,h).

Figure 4

Light micrographs of colonies with ambiguous morphology. (a) Calcified hemispherical GDL1 colony from the Guadiela River. (b) Section of the MU4 colony from the Muga River showing layers. (c) Slightly irregular-hemispherical and calcified BAT4 colony from the Bogarra River. (d) Zonation with distinct pigmentation in the decalcified BAT4 colony. (e) Large proportion of isopolar filaments without heterocysts within the GDL1 colony. (f) Heterogeneity in the trichomes found in the BAT4 colony. (g) Detail of isopolar filaments without heterocysts within the GDL1 colony. (h) Calothrix filament found in the BAT2 colony from the Bogarra River. Bars, 1 mm (a–c), 200 μm (d), 100 μm (e,f), 20 μm (g,h).

Figure 5

Light micrographs of the BAT13 colony from the Bogarra River. (a) Calcified hemispherical colony. (b) Dichotomic and radial arrangement of filaments. (c) Bunch of trichomes, some of them showing a funnel-like end. (d) Dichotomic arrangement with false branches. (e) Sheaths distinctly broader than the trichome, showing an intercalary heterocyst. (f) Secondary trichomes remaining within the ‘mother’ sheath. In a filament, three trichomes in a common sheath (arrow). (g) Thick yellow–brown sheath with a trichome tapering into a hyaline hair. (h) Filament of Calothrix found inside the sample. (i) Lamellated sheaths. Bars 1 mm (a), 100 μm (b,c), 20 μm (d–i).

Photographs and light micrographs of n class="Disease">Rivularia biasolettiana-type colonies. (a) BAT5 and (b) BAT14 colonies from the Bogarra River. (c) GG2 colony from the Guarga River. (d) Radial arrangement of filaments inpan> the BAT5 colony from the Bogarra River. (e) Detail of the radial arrangement of filaments inpan> the END5 colony from the Endrinpan>ales River. (f) and (g) BAT12 filaments showinpan>g n class="Disease">pigmented or hyaline sheaths. (h) Hairs in filaments of the GG2 colony from the Guarga River. (i) Meristematic zones showing divided trichomes persisting within common old sheaths in END5 from the Endrinales River. Bars 1 mm (a,b), 200 μm (d), 100 μm (e), 20 μm (f–i).

Light micrographs of Cyanomargarita colonies. (a) Hemispherical END1 colony from the Endrinpan>ales stream. (b) Section of the END1 colony showinpan>g zonation. (c) Radial arrangement of filaments inpan> the ARA4 colony from the Aras River. (d) Layers with distinpan>ct pigmentation in the decalcified END8 colony from the Endrinales stream. (e) Tapering trichomes in the END8 colony from the Endrinales stream, similar to those of Rivularia. (f) Parallel and densely arranged filaments in the END1 colony from the Endrinales stream. Colored and lamellated sheaths of filaments in the ARA4 colony from the Aras River and (g) hyaline sheaths in other parts of the same ARA4 colony (h). Bars 1 mm (a,b), 200 μm (c,d), 100 μm (e,f), 20 μm (g,h).

Light micrographs of colonies with ambiguous morphology. (a) Calcified hemispherical GDL1 colony from the Guadiela River. (b) Section of the MU4 colony from the Muga River showing layers. (c) Slightly irregular-hemispherical and calcified BAT4 colony from the Bogarra River. (d) Zonation with distinct n class="Disease">pigmentation inpan> the decalcified BAT4 colony. (e) Large proportion of isopolar filaments without heterocysts withinpan> the GDL1 colony. (f) Heterogeneity inpan> the trichomes found inpan> the BAT4 colony. (g) Detail of isopolar filaments without heterocysts withinpan> the GDL1 colony. (h) n class="Species">Calothrix filament found in the BAT2 colony from the Bogarra River. Bars, 1 mm (a–c), 200 μm (d), 100 μm (e,f), 20 μm (g,h).

Light micrographs of the BAT13 colony from the Bogarra River. (a) Calcified hemispherical colony. (b) Dichotomic and radial arrangement of filaments. (c) Bunch of trichomes, some of them showing a funnel-like end. (d) Dichotomic arrangement with false branches. (e) Sheaths distinctly broader than the trichome, showing an intercalary heterocyst. (f) Secondary trichomes remaining within the ‘mother’ sheath. In a filament, three trichomes in a common sheath (arrow). (g) Thick yellow–brown sheath with a trichome tapering into a hyaline hair. (h) Filament of n class="Species">Calothrix found inpan>side the sample. (i) Lamellated sheaths. Bars 1 mm (a), 100 μm (b,c), 20 μm (d–i).

Macroscopic n class="Species">environmental samples analyzed inpan> this study.

Nine colonies (BAT5, BAT12, BAT14, END5, GG1, GG2, MU5, GOR1 and GOR3) showed the typical characteristics of R. biasolettiana[7], such as soft gelatinous colonies, an easily crushed structure, and occasional encrusting by calcareous particles (Fig. 1a–c). The trichomes gradually narrowed (Fig. 1d–i), elongating into long hyaline hairs (Fig. 1h,i). In meristematic zones, divided trichomes persisted within common old sheaths (Fig. 1f–i). Seven colonies (GOR4, GOR5, END2, END15, HOY3, HOY5 and n class="CellLine">HOY14) corresponded clearly to R. haematites[7], with highly calcified and hard hemispherical colonies, with concentric layers (Fig. 2a,b) displayinpan>g parallel filaments that were radially and densely arranged (Fig. 2c–f) and sections showinpan>g obvious zonation (Fig. 2c,d). As inpan> R. biasolettiana, the trichomes gradually narrowed, endinpan>g inpan> hyalinpan>e hairs (Fig. 2e–g), and new trichomes persisted withinpan> common sheaths (Fig. 2h). The dimensions of trichomes, filaments and heterocysts are shownpan> inpan> Table 2. Although some colonies of R. haematites showed slightly wider cells than those found inpan> R. biasolettiana colonies, with greater variability (Table 2), the mean trichome diameters, which ranged from 3.9–5.6 μm inpan> R. haematites and 4–4.7 μm inpan> R. biasolettiana, did not show significant differences (p > 0.05).

Table 2

Morphological characteristics of Rivularia-like colonies with a dominant morphotype.

Measurements are given as mean ± standard deviation (range) in μm. ND: Not Determined.

Seven other colonies (GOR11, GOR12, OSI3, ARA4, GOR2, END1 and END8) were also hemispherical, some of them soft and gelatinous and others highly calcified with sections showing zonation (Fig. 3a–d). The trichomes also showed the typical tapering of those in Rivularia colonies and other similar morphological characteristics (Fig. 3a–h). However, the main difference between these colonies and the previously analyzed colonies was the size of the cells (Table 2, Fig. 3g,h), which were clearly wider in these colonies (significant differences, p < 0.05). The mean trichome diameter at the filament base ranged from 7.8 to 10.1 μm. The heterocysts were also clearly larger (Table 2). These features corresponded with those of the n class="Disease">new genus Cyanomargarita[15]

However, four Rivularia-like colonies (MU4, GDL1, BAT2 and BAT4) showed ambiguous morphology, varying in the degree of n class="Disease">calcification anpan>d zonation (Fig. 4a–d) as well as displayinpan>g high heterogeneity inpan> the trichomes (Fig. 4e–h). For inpan>stanpan>ce, GDL1 was a highly calcified colony with a certainpan> degree of zonation, anpan>d most of the filaments were of the Rivularia type, but there was a considerable proportion of other morphotypes withinpan> the colony, such as thinpan>ner anpan>d nontapered trichomes, without heterocysts, that were found between the Rivularia filaments anpan>d sometimes emerginpan>g outside the colony (Fig. 4a,e,g). The MU4, BAT2 anpan>d BAT4 colonies also presented filaments anpan>d trichomes with very different sizes anpan>d shapes inpan> the same colony (Fig. 4b–d,f,h). In BAT4, clear zonation could be observed (Fig. 4d,f), as well as a large number of filaments without heterocysts (Fig. 4f).

Microscopic examination of the hemispherical and calcified BAT13 colony (Fig. 5a) showed features different from those of the previously analyzed colonies (Fig. 5b–i). Most of the filaments did not taper, although this was due to the presence of a wide and colored sheath (Fig. 5b–i). When observed in detail, the trichomes narrowed from the base, which presented a heterocyst, to the apex (Fig. 5c–g). Although this colony appeared macroscopically as a Rivularia colony (Fig. 5a), the trichome arrangement resembled that in the genus Dichothrix[7], such as subdichotomic falsely branched filaments, where secondary trichomes remained within the ‘mother’ sheath (Fig. 5c,d,f). Some filaments showed a bunch of trichomes, open at the end with a funnel-like ending (Fig. 5c). The sheaths were distinctly broader than the trichomes (Fig. 5d–i), often lamellated (Fig. 5e,i), and frayed but closed at the ends (Fig. 5g). The trichomes displayed thin cells in the thick yellow–brown sheath that were quadratic or shorter than wide at the end, tapering into a hyaline hair (Fig. 5e–g). The heterocysts were basal and mainly conical (Fig. 5d,f), but some intercalary and cylindrical heterocysts could be observed (Fig. 5e). Filaments of n class="Species">Calothrix were also found inpan>side the sample (Fig. 5h).

Finally, sample MUD1 showed the typical characteristics of the genus Dichothrix[7], such as macroscopic brush-like n class="Disease">fasciculated tufts encrusted by calcareous precipitate (Fig. 6a–d) anpan>d filaments inpan> a characteristic dichotomic arranpan>gement that were repeatedly falsely branpan>ched (Fig. 6a,b). The filaments were tapered anpan>d had strong lateral false branpan>chinpan>g adjacent to heterocysts (Fig. 6c,d). The branpan>ches formed inpan>dividual sheaths anpan>d diverged from the basal filament inpan> parallel, anpan>d the new trichome shared the sheath with the old trichome inpan> the basal part (Fig. 6c,d). The sheaths were firm, yellow to brownpan>, anpan>d lamellated inpan> only some filaments (Fig. 6d). The trichomes gradually narrowed towards the apex, with barrel-shaped cells (Fig. 6c,d). No hairs were observed. The basal heterocysts were hemispherical or barrel-shaped with a characteristic inpan>tense blue-green color (Fig. 6d).

Figure 6

Light micrographs of a Dichothrix tuft from the Muga River. (a) Brush-like fasciculated MUD1 tuft encrusted by calcareous precipitate. (b) Dichotomic arrangement with repeated false branches. (c) Lateral false branching adjacent to heterocysts. (d) Decalcified filaments showing a new trichome sharing the sheath with the old trichome in the basal part. Bars 200 μm (a), 100 μm (b), 20 μm (c,d).

Light micrographs of a Dichothrix tuft from the Muga River. (a) Brush-like n class="Disease">fasciculated MUD1 tuft encrusted by calcareous precipitate. (b) Dichotomic arranpan>gement with repeated false branpan>ches. (c) Lateral false branpan>chinpan>g adjacent to heterocysts. (d) Decalcified filaments showinpan>g a new trichome sharinpan>g the sheath with the old trichome inpan> the basal part. Bars 200 μm (a), 100 μm (b), 20 μm (c,d).

Cyanobacterial taxonomic assignments

The results of Illumina sequencing that targeted the V3-V4 hypervariable region of the 16S rRNA gene from all the collected samples revealed in total 25 OTUs present at an abundance of 1% or more in at least one of the colonies. OTUs were numbered in order of decreasing abundance, taking into account all the colonies. The first two OTUs accounted for 81% and the first 10 accounted for 95% of all the reads, considering all the colonies together. Dedicated phylogenetic trees constructed with our sequences from cultures and field samples and those downloaded from the NCBI database (Fig. 7) allowed us the taxonomic assignment of these OTUs, as previously carried out[27,28].

Figure 7

Phylogenetic trees obtained by the neighbor-joining method representing (a) heterocystous cyanobacteria and (b) filamentous nonheterocystous cyanobacteria, based on the analysis of the 16S rRNA gene, showing the position of the operational taxonomic units (OTUs) and the sequence obtained by cloning a Dichothrix environmental sample obtained from the present study (in bold). Numbers near nodes indicate bootstrap values greater than or equal to 50.

Phylogenetic trees obtained by the neighbor-joining method representing (a) heterocystous cyanobacteria and (b) filamentous nonheterocystous cyanobacteria, based on the analysis of the 16S rRNA gene, showinpan>g the position of the operational taxonomic units (OTUs) and the sequence obtainpan>ed by cloninpan>g a Dichothrix environmental sample obtained from the present study (in bold). Numbers near nodes indicate bootstrap values greater than or equal to 50.

Fourteen OTUs were mapped to the heterocystous subtree (Fig. 7a). The most abundant OTU (OTU1) fell into a very well-supported cluster with other Rivularia sequences. The percent identity between OTU1 and the other sequences inpan> this cluster ranged from 97.6 to 100%, with the OTUs beinpan>g 100% similar to an environmental colony collected from the Alharabe River in southwestern Spain[11] and to other environmental samples isolated from the Baltic Sea[29]. Thus, OTU1 was assigned to Rivularia sp. OTUs 2 and 13 also fell in a very well-supported cluster with Cyanomargarita melechinii and Cyanomargarita calcarea. OTU2 was more similar to C. melechinii (99.52%), while OTU13 was more similar to C. calcarea (98.07%). Both OTUs were assigned to Cyanomargarita sp. OTUs 3, 11, 14, and 26 clustered with other Calothrix sequences; thus, they were assigned to this genus. OTUs 20 and 4 were included in a cluster with Macrochaete strains and were assigned to this genus; OTU4 was 98.3% similar to Macrochaete lichenoides, and OTU20 was 96.4–96.63% similar to Macrochaete psychrophila. OTU6 was mapped to a cluster that included other Calothrix sequences and Scytonematopsis contorta strains, with similarities ranging from 95.9 to 98.3%, as well as other environmental sequences obtained from Dichothrix tufts from the Muga River, which were 99.5% similar; therefore, it was assigned to Dichothrix sp. OTU8 was assigned to Scytonema sp. since it mapped to a well-supported clade with other Scytonema sequences. OTU19 clustered with other sequences of Nostoc and was assigned to this genus, while OTU15 was mapped to a sister clade of Anabaena, Nostoc and Tolypothrix strains and was therefore assigned only to the Nostocaceae family. Finally, OTU9 mapped to a cluster with an uncultured bacterium, and the maximum similarities found in the NCBI database were 95.22 with an uncultured bacterium and 93.78 with Calothrix sp. CAL3363[29]; therefore, this OTU was assigned to the Nostocales order.

Regarding the nonheterocystous cyanobacteria, eleven OTUs mapped to this subtree (Fig. 7b). The most abundant OTUs, OTU5 and OTU7, fell in two well-supported clusters with Oculatella strainpan>s and Phormidium strainpan>s, respectively. OTUs 16, 17, 18, 24 and 27, assigned to Leptolyngbya sp., mapped to clades with other Leptolyngbya sequences. OTU28 clustered with other Schizothrix strains. OTU10 and OTU21 could be assigned only to Leptolyngbyaceae and Oscillatoriales, respectively, due to their low percent identity with other sequences in the databases. Finally, OTU12 remained unassigned since no match was found in the databases for this sequence, and there was no clustering with any close relatives in the phylogenetic tree (Fig. 7b).

Phylotype diversity in individual colonies

Both types of identified Rivularia colonies, R. biasolettiana and R. haematites, showed a clear dominance of OTU1 (Fig. 8). In six of the nine colonies identified as R. biasolettiana, OTU1 presented abundances from 97 to 99%, and in three, this proportion decreased to 76.8–93%. In six of the seven colonies of the R. haematites type, the abundance of OTU1 ranged from 97 to 99.8%, and in one colony, the abundance was 85.5% (Fig. 8). OTU3, corresponding to Calothrix sp., and OTU5, correspondinpan>g to Oculatella sp., were other phylotypes found in these colonies, with abundances ranging from 1.4–8.6% for Calothrix and 1.5–20.9% for Oculatella (Fig. 8).

Figure 8

Phylotype diversity in individual colonies. The operational taxonomic units (OTUs) are represented by different colors and corresponding numbers. The colors correspond to those in Fig. 7. See Table 1 for the names and geographical origins of the environmental samples.

Phylotype diversity in individual colonies. The operational taxonomic units (OTUs) are represented by different colors and corresponding numbers. The colors correspond to those in Fig. 7. See Table 1 for the names and geographical origins of the n class="Species">environmental samples.

In the seven Cyanomargarita colonies, OTU2 dominpan>ated, ranginpan>g from 97.1 to 99.2% inpan> 4 colonies, decreasinpan>g to 86.6% inpan> another colony, and further decreasinpan>g to 67.6 and 57.28% inpan> the other two colonies. Regardinpan>g the other phylotypes found inpan> these colonies, OTU7, correspondinpan>g to Phormidium sp., was the most abundant and present in all the colonies, with abundances of 12% and 13.5% in two of the colonies (Fig. 8). A phylotype corresponding to Calothrix sp., found in previously analyzed Rivularia colonies (OTU3), was also found in a colony of Cyanomargarita (GOR2), with an abundance of 25%. OTU13, which corresponded to another phylotype of Cyanomargarita, was present in only one colony (END1), with a 13.5% abundance.

The four Rivularia-like colonies with ambiguous morphologies were the most variable in terms of phylotype composition (Fig. 8). In the MU4, GDL1 and BAT2 colonies, Rivularia sp. (OTU1) predominated, although at different proportions. In the MU4 colony, OTU1 accounted for 72% of the total abundance, but Oculatella sp. (OTU5, 8.37%) and Calothrix spp. (OTU11 and OTU3, 8% overall) coexisted. In GDL1, the abundance of OTU1 was 59.4%, and that of unassigned OTU12 was 20.6%, which corresponded to the large proportion of other filaments observed under the microscope (Fig. 4e,g). This colony also contained Leptolyngbya sp. (OTU17), with an abundance of 7.3%, and Phormidium sp. (OTU7), with an abundance of 6.6%. The BAT2 colony, in addition to 63.4% OTU1, contained 8.6% Calothrix sp. (OTU3) and 16.5% Nostocales OTU9 (Fig. 8).

Despite its macroscopic similarity to the Rivularia colonies and clear banded appearance (Fig. 4d,f), BAT4 presented a negligible abundance of OTU1 (0.06%). This colony was composed of several OTUs at different proportions, such as Calothrix phylotypes correspondinpan>g to OTUs 3, 11 and 14 (22.2%, 15.3%, and 13.2%, respectively), Nostocales OTU9 (15%), Leptolyngbyaceae OTU10 (24%), and, to a lesser extent, Nostocaceae OTU15 (4.5%) and Leptolyngbya OTU18 (4.3%) (Fig. 8).

The Rivularia-like BAT13 colony also presented a negligible abundance of OTU1 (0.6%) and was dominated by OTU4 (76%), which was phylogenetically similar to the new genus Macrochaete. This colony also harbored, albeit to a lesser extent, OTUs 3 and 14, correspondinpan>g to Calothrix (6.7% and 4.2%, respectively), and Nostocales OTU9 (6.6%) (Fig. 8).

The MuD1 tuft was composed mainly (53.2%) of OTU6, assigned to Dichothrix sp., followed by OTU8 (Scytonema sp., 35.2%), OTU7 (Phormidium sp, 4.6%), and at a small proportion, OTU19 (Nostoc sp., 1.6%) and OTU24 (Leptolyngbya sp., 1.2%) (Fig. 8).

Discussion

Genotypic heterogeneity in single Rivularia-like colonies

Rivularia-like colonies have a global distribution, occurring in marine or freshwater habitats, where they are usually attached to a rocky substrate; however, many studies have reported that Rivularia spp. are associated with unpolluted environments[14]. In addition, the relationships between some morphological or physiological features and the environment make these species excellent environmental indicators of changes in running water quality, mainly related to eutrophication processes[14,30]. Therefore, they have been included in biomonitoring programs[21,31,32]. On the other hand, because Rivularia colonies sometimes persist for very long periods, avoiding grazing, the toxicity of these colonies is being investigated[33]. It is undoubted that in all of these approaches, where genera and species must be strictly identified from environmental samples, accurate cyanobacterial characterization is essential.

Traditional identification of cyanobacteria involves assigning a colony to a morphospecies, and conventionally, a bacterial colony is defined as a visible mass of clonal microorganisms, all of which originated from a single cell. However, the results from the present study show that the majority of the analyzed colonies consist of different clones growing together. Among the 28 Rivularia-like colonies, the phylotype corresponding to Rivularia sp. was present in 19 colonies, with abundances ranging from 59.4 to 99.8% depending on the studied colony. Nevertheless, it should also be noted that in most of the colonies, this phylotype dominated, whereby in 14 colonies, it presented an abundance of ≥ 90% (and within 7 of these colonies, the abundance was close to 99%). However, in three colonies, the abundance ranged from 72 to 85%, and in two of them, the abundance decreased to approximately 60%. The other highly abundant phylotypes found in these colonies, which reached abundances up to approximately 21%, corresponded to Calothrix sp. and Oculatella sp., the latter a genus morphologically similar to Leptolyngbya but separated from it because of genetic differences[34]. These results indicated great variability in the abundance of the phylotype corresponding to Rivularia depending on the analyzed colony, as well as variation in the other phylotypes and their abundances found in these colonies.

One of the surprising findings was that among the twenty-eight analyzed Rivularia-like colonies, seven corresponded to the new, recently described genus Cyanomargarita, which as the authors described, is virtually inpan>distinpan>guishable from Rivularia inpan> field samples[15]. In these colonies, genotypic heterogeneity was also found, inpan> which the abundance of the phylotype correspondinpan>g to Cyanomargarita varied from 57,28% in a colony with clear lamination resembling R. haematites (see Fig. 3b) to 99.2% in a soft colony resembling R. biasolettiana. Interestingly, in these colonies, Phormidium sp. was the dominant nonheterocystous cyanobacterium instead of Oculatella from Rivularia colonies, but the phylotype corresponding to Calothrix was also found.

Furthermore, phylotypes corresponding to n class="Species">Cyanomargarita and Rivularia were never found together inpan> the same colony, although both types of colonies coexisted inpan> the same rivers (e.g., Gordale Beck and Enpan>drinpan>ales). Allelopathic effects could explainpan> these results, as previously suggested for other cyanobacteria[35]. In fact, García-Espín et al.[33] showed that extracts obtainpan>ed from Rivularia colonies affected the photosynpan>thetic activity of several diatoms and a red alga. Further experiments with extracts from both colonies would confirm this possible effect.

Another very surprising finding was that two Rivularia-like colonies did not present any phylotypes corresponding to Rivularia or Cyanomargarita (or containpan>ed them at an abundance ≤ 0.7%). In one of these colonies (colony BAT4), five different phylotypes were found at similar abundances (approximately 15–20%), of which three corresponded to different Calothix spp. and the others corresponded to other Nostocaceae and Leptolyngbyaceae. In the other colony (BAT13), the dominant phylotype corresponded to the new genus Macrochaete[16]. This genus has been described only from cultures, so to the best of our knowledge, this is the first report in which a natural population is morphologically and genetically characterized. Nevertheless, it is noteworthy that the morphological characteristics of filaments and trichomes in this environmental sample were different from those reported in the description of this new genus, in which the phenotypic features resembled those of Calothrix. However, these features corresponded only to isolated strains, which are known to exhibit morphological variability and differences from natural populations[7,12,13].

R. biasolettiana vs R. haematites

However, what was very interesting and deserves to be highlighted is that when we tried to differentiate the two typical Rivularia colonies found in calcareous streams, R. biasolettiana and R. haematites, we did not find genetic differences, at least at the studied level, the 16S rRNA gene.

16S rRNA is the most widely used marker gene[36,37], which n class="Disease">fits the criteria of ubiquity, regions of strong conservation, and regions of hypervariability[38,39]. This gene is supported by reference databases containpan>inpan>g over a million full-length 16S rRNA sequences, therefore spanninpan>g a broad phylogenetic spectrum[40]. The 16S rRNA gene has served as the general framework and as the benchmark for the taxonomy of prokaryotes[41]. Advances inpan> high-throughput sequencinpan>g technologies have enabled almost comprehensive descriptions of bacterial diversity through 16S rRNA gene amplicons, which have been used inpan> surveys of microbial communities to characterize the composition of microorganisms present inpan> environments worldwide[42-45]. Although some issues have been raised, such as identification of metabolic or other functional capabilities of microorganisms when studies focus only on this gene, recent studies have shownpan> that the phylogenetic inpan>formation containpan>ed inpan> 16S marker gene sequences is sufficiently well correlated with genomic content to yield accurate predictions when related reference genomes are available[46-49]. Therefore, the 16S rRNA gene continpan>ues to be the mainpan>stay of sequence-based bacterial analysis, vastly expandinpan>g our understandinpan>g of the microbial world[50].

In particular, in cyanobacteria, as in other prokaryotes, the 16S rDNA gene is currently the most commonly used marker for molecular and phylogenetic studies[51,52]. The information obtained from 16S rDNA gene phylogenetic reconstructions, together with morphological, ultrastructural, and ecological data, led Komárek et al.[53] to propose the current accepted classification of cyanobacteria. There have also been specific studies by this group concerning the problems associated with single-gene phylogenies, in which robust phylogenomic trees of cyanobacteria derived from multiple conserved proteins have also shown congruence between the multilocus and 16S rRNA gene phylogenies, which once again demonstrates the considerable strength of the 16S rRNA gene for phylogenetic inference and evaluation of prokaryote diversity[54-57].

In this study, in contrast to the genetic identity found in R. biasolettiana and R. haematites colonies, showing a dominance of OTU1, the remainder of the studied representatives of Rivulariaceae showed a wide range of variation in the 16S rDNA sequences and with OTU1. Sequence identity between OTU1 and the remaining OTUs belonging to this family was as low as approximately 90%, ranging from 90.73 to 93.41%, and when it was compared with other Rivulariaceae from the databases, in the different clusters of the phylogenetic tree, this value ranged from 87.12 to 93.90%. A large difference between the sequences of this gene was also found in other studies on Rivulariaceae[15-17,29,58]. In fact, several new genera are emerging on the basis of these differences[15-17]. Comparisons of phylogenies using other markers, such as the phycocyanin operon and the intervening intergenic spacer (cpcBA-IGS) with the 16S rRNA gene in previous studies in Rivulariaceae, have shown largely consistent results, with a high level of divergence between the components of this family[11].

In addition, the results of the present study showed correlations between morphological characteristics and the analyzed genes in all the cyanobacterial colonies/tufts, except for those of R. biasolettiana and R. haematites. In these two cyanobacteria, only distinct macroscopic phenotypic features were observed due to zonation and different degrees of n class="Disease">calcification sinpan>ce no significant differences were found inpan> the size measurements or other microscopic characteristics.

Therefore, although the remainder of the genome has not been studied in these populations, the genetic identity of the studied marker, phenotypic features, together with n class="Species">environmental preferences poinpan>t out that R. biasolettianpan>a anpan>d R. haematites are ecotypes of the same species, as previously suggested[59].

R. biasolettiana and R. haematites have very similar morphotypes, and traditional taxonomical classification and studies have distinguished them primarily by their degrees of calcification. R. biasolettiana-type colonies are described as more gelatinpan>ous and less calcified, and the crystals are disseminpan>ated; however, R. haematites colonies are very hard and exhibit extensive calcification in concentric zones, which leads to clear lamination[24,25,60,61]. Because of its heavy mineralization, R. haematites is a model for stromatolite-binding organisms[25,26].

Microscopic observations from this study showed that some colonies presented typical R. haematites morphology with concentric bands of intense calcification (see Fig. 2a,b), and others were soft and less calcified, such as R. biasolettiana, although all of them presented the same dominpan>ant phylotype. Many others with this dominpan>ant phylotype have also shownpan> ambiguous morphology with no clear laminpan>ation, although some dark/light zones could be observed (see, e.g., Fig. 4b,d, f). Even inpan> Cyanomargarita colonies, whose genotype was clearly separated from that of Rivularia, concentric zones and extensive calcification could be observed (see, e.g., Fig. 3b,d). These results suggested that these phenotypic features are not diagnostic characteristics for further identification.

In a two-year study, Obenlüneschloss and Schneider[61] found that not all analyzed R. haematites colonies showed distinct concentric calcification layers. In the stromatolites of both types of Rivularia, the same laminpan>ation was observed, and the differences inpan> calcification appeared later[60]. Pentecost and Franke[26] compared populations of R. biasolettiana and R. haematites and argued that although both could be distinguished by their form of calcification and their trichome diameter, some populations of R. biasolettiana were more intensely calcified than others, suggesting that a continuity of forms may exist, even within the same stream, and therefore, a continuum of colony forms probably occurs between these taxa.

Differences in the calcification patternpan> have been attributed to seasonality and cyanobacterial activity, inpan> particular to photosynpan>thesis[24,26,62]. The calcification in R. haematites occurred in concentric bands, which varied in thickness and the density of crystals. Since characteristic zonation is formed by filaments of different successive generations, the thickness will vary depending on the growth rate, while crystal density will depend on the rate of calcification. Calcification is the result of photosynthesis (with a maximum of 14%) and evaporation during the warmer seasons, while it is entirely abiogenic during winter as a result of CO2 evasion[63]. Therefore, dense calcified bands similar to those formed in winter have been described that are caused by a reduction in trichome growth and EPS production, allowing the development of abiotic surface precipitate, and less calcified layers are formed during spring and summer, when calcification is associated with photosynthesis in zones of growth with cell division[24,26]. Thus, differences in climatic conditions and/or biological activity seem to lead to differences in the degrees of zonation and calcification.

The growth of Rivularia colonies is seasonal and strongly correlated with water temperature[24,26]. The colony growth rates were 12–14 µm/day inpan> summer and 2 µm/day inpan> winpan>ter[24]. The occurrence of R. biasolettiana was more closely related to high temperatures than that of R. haematites[21]. Moreover, colonies of R. haematites were generally collected under temperatures below 15 °C inpan> mountainpan> runninpan>g waters[64], and R. haematites stromatolites have been described as preferentially developed in wet periods, particularly in autumn and winter[60]. Our own field observations during the sampling for this and previous studies were that the gelatinous and weakly calcified R. biasolettiana type was more abundant in warmer locations, and in contrast, R. haematites was dominant in cold locations (data not shown).

One possible explanation for the results found in this study could be related to these differences in the degree of zonation and calcification inpan> relation to climate, which could inpan>clude microclimatic conditions. In warmer sites or climatic conditions, when growth is rapid, the number of filaments will inpan>crease, movinpan>g towards the surface inpan> a weakly dense and unaligned arrangement, on which calcite crystals spread, providinpan>g a lighter and less calcified structure. Thus, inpan>creased growth of Rivularia colonies can lead to the R. biasolettiana type. Under colder conditions, such as inpan> winpan>ter, or microclimatic conditions, when growth slows downpan> for other reasons, such as low light, filaments become more densely packed, allowinpan>g the development of extensive precipitates and leadinpan>g to a dark band. When these conditions change, e.g., inpan> the sprinpan>g and summer, inpan>creases inpan> temperatures and/or light will result inpan> inpan>creasinpan>g and faster growth, leadinpan>g to a less calcified new layer, and successive seasonal and/or microenvironmental changes will result in the typical lamination of R. haematites. Therefore, warmer places with high temperatures and/or light will allow the occurrence of the R. biasolettiana type, while in colder sites and/or sites with alternating environmental conditions, the R. haematites type will develop. Shaded colonies and colonies that lie in the supratidal spraywater zone often contain small, irregular and more densely packed crystals[61].

Cyanobacteria are known to modify EPS production, pigments, and morphology under environmental stimuli[6]. The production of EPS also varies depending on the cyanobacteria, whereby Rivularia has shown a well-developed exopolymer layer[65], which is of great importance for this epilithic cyanobacteria, as it acts as an adhesive that allows cells to stick to the stones in the running waters, and it holds the filaments together, minimizing cell damage during intermittent drying exposure to the air and evaporation in the warmer seasons[66]. The C/N ratio is an important parameter for the variation in EPS production since high amounts of fixed C compared to N levels drive EPS synthesis to store excess C[67,68]. Therefore, Rivularia colonies that are exposed, in spring and summer, to high light intensities and temperatures will increase their photosynthetic rates and therefore the amount of EPS, as shown by the R. biasolettiana morphotype. In addition, most of the analyzed populations were dark in color, probably in relation to the accumulation of the yellow–brown scytonemin pigment in the sheaths or EPS, as previously observed in shallow and clear oligotrophic ecosystems, where water clarity allows UV radiation to penetrate well, protecting the cells from the damaging effects of this radiation[69,70].

In conclusion, environmental factors can lead to differences inpan> macroscopic phenotypic features, such as those found inpan> the Rivularia colonies studied here. However, further samplinpan>g under different climatic conditions and/or microenvironmental conditions or of Rivularia cultures grown under distinct temperature and/or illumination conditions, as well as analysis of other genes, are needed to confirm this hypothesis.

Methods

Sampling

The locations of the sampling sites from which samples were collected and their codes are shown in Table 1. All the sampled rivers or streams were characterized by highly calcareous waters. The Muga, Guarga, Osia, and Arás rivers are located in northeastern Spain, the Hoyas and Endrinales streams and Bogarra River are located in southeastern Spain, and the Guadiela River is located in central Spain. The Gordale Beck sampling site was located near Malham, West Yorkshire, northern England, from which Rivularia haematites has been reported[24,26]. From these locations, twenty-one Rivularia-like colonies were sampled in Spain, and seven in the United Kingdom. In addition, a Dichothrix tuft was collected from the Muga River, Spain. The samples were kept cold until reaching the laboratory, where they were divided into two parts, after washing them and checking by microscopy that there were no cyanobacterial contaminants outside the colonies. One part from each sample was used for morphological characterization and the other frozen and stored at − 20 °C until DNA extraction for genetic characterization. The colonies or tuft were named after the river or stream where they were collected, followed by a number (Table 1).

Morphological characterization

Samples were inspected under a Leica MZ12.5 dissecting stereomicroscope (Leica, Leica Microsystems, Wetzler, Germany) equipped with epifluorescence and video camera systems and by an Olympus BH2-RFCA photomicroscope (Olympus, Tokyo, Japan) equipped with phase-contrast, epifluorescence, and video camera systems (Leica DC Camera, Leica Microsystems). To better observe the samples via microscopy, several colonies were decalcified with 0.5 M n class="Chemical">EDTA. Representative colonies of Rivularia-like samples were analyzed, except those with ambiguous morphologies, for which the variability of the morphotypes found withinpan> the colony precluded analysis. Size measurements were analyzed usinpan>g SigmaScan Pro 5.0.0 software. Kruskal–Wallis one-way analysis of variance of ranks was used to determinpan>e the significance of differences between size measurements.

Genetic characterization

Genomic DNA was extracted from individual colonies using a Power Biofilm DNA Extraction Kit (Mo Bio, Carlsbad, CA, United States) following the manufacturer’s instructions, with a modification at the beginning of the protocol as previously described[28] to improve the lysis of the cells.

The phylotype composition of the cyanobacterial colonies was assessed by amplicon metagenomics targeting the hypervariable V3-V4 region of the 16S rRNA gene, using an Illumina MiSeq sequencer (Illumina Inc., San Diego, CA, USA) at the Genomic Service of the Universidad Autónoma de Madrid. First, PCR was performed using the cyanobacterial-specific primers CYA359F and 781Ra/781Rb[71] in separate reactions for each reverse primer as suggested by Boutte et al.[72] plus a targeted sequence. PCR was carried out with 1 ng of DNA, Q5 Hot Start High-Fidelity DNA Polymerase (New England Biolabs), and 100 nM primers in a 25 μl volume, and the cycling conditions were 1 × 98 °C for 30 s, 23 × 98 °C for 10 s, 54 °C for 20 s, and 72 °C for 20 s, and 1 × 72 °C for 2 min. The second PCR using barcoded primers for each colony was performed in a 20 μl final volume using the same DNA polymerase, 1 μl of the first PCR product, and 400 nM primers with the following cycling conditions: 1 × 98 °C for 30 s, 7 × 98 °C for 10 s, 60 °C for 20 s, and 72 °C for 20 s, and 1 × 72 °C for 2 min.

PCR products were quantified, pooled in equimolar amounts and purified using AMPure Beads (Beckman Coulter) prior to sequencing with a MiSeq sequencer (Illumina Inc., San Diego, CA, USA) at a read length of 2 × 300 bp. At least 100,000 sequences were obtained for each amplicon.

Sequence data were processed using QIIME v.1.9.0[73] as previously described[28]. The first taxonomical assignment of the OTUs was performed against the Greengenes database[74] by the classifier method of the Ribosomal Database Project with a confidence value of 0.8[75], which allowed the removal of OTUs identified as chloroplasts or noncyanobacterial organisms. Afterwards, OTUs were matched against our sequence dataset of isolated cultures and field samples by employing the ‘uparse ref command’ in USEARCH[76]. In addition, a previously sampled Dichothrix field tuft from the Muga River was analyzed by cloning almost the entire 16S rRNA gene, as previously described[16]. Then, all this information was compared with the taxonomic assignments made against the Greengenes database[74] as mentioned above and against the SilvaMod database[77] using the lowest common ancestor (LCA) algorithm implemented in CREST[78]. In addition, the representative OTU sequences were compared with those in the NCBI database using a BLAST search (https://www.ncbi.nlm.nih.gov/blast), and sequences similar to them were downloaded to construct phylogenetic trees as previously described[27,28]. The first tree was constructed with only full-length 16S rDNA sequences (approximately 1500 bp), which were aligned using ClustalW in BioEdit 7.0.5.3[79]. After this, the OTU sequences (approximately 420 bp) were aligned against the alignment of the first tree, and a new tree was constructed and compared with the previous tree to ensure that the clades were maintained. Phylogenetic trees were computed using the neighbor-joining method[80] in Mega 7[81] with 1000 bootstrap replicates. Evolutionary distances were computed using the Tajima-Nei method[82], and pairwise deletion was used to account for sequence-length variation and gaps. The percent identity between sequences was determined as (1-p-distance)*100.

Because OTU1 appeared at markedly high abundance, amplicon sequence variant (ASV) determination was performed using the DADA2 pipeline in QIIME 2[83], showing that ASVs assigned to this OTU differed by only one nucleotide and were therefore indistinctly distributed between the different samples.

Alpha diversity indices (Chao1 estimator, Good’s coverage and observed OTUs) were calculated using QIIME. Good’s coverage estimates reached 100% in all the samples, indicating that the large majority of the cyanobacterial diversity was captured.

The OTU sequences have been deposited in the GenBank database under accession numbers MT335702-MT335726. Raw sequencing data have been deposited in the NCBI Sequencing Read Archive under accession number PRJNA648107.