Epilithic cyanobacterial communities of a marine tropical beach rock (Heron Island, Great Barrier Reef): diversity and diazotrophy

Aerosol sources and transport paths co-control the atmospheric bacterial diversity over the coastal East China Sea

Airborne bacteria along with chemical composition of aerosols were investigated during five sampling seasons at an offshore island of the East China Sea. Bacterial diversity was the lowest in spring, the highest in winter, and similar between the autumns of 2019 and 2020, suggesting remarkably seasonal variation but little interannual change. Geodermatophilus (Actinobacteria) was the indicator genus of mineral dust (MD) showed higher proportion in spring than in other seasons. Mastigocladopsis_PCC-10914 (Cyanobacteria) as the indicator of sea salt (SS) demonstrated the highest percentages in both autumns, when the air masses mainly passed over the ocean prior to the sampling site. The higher proportions of soil-derived genera Rubellimicrobium and Craurococcus (both Proteobacteria) and extremophile Chroococcidiopsis_SAG_2023 (Cyanobacteria) were found in summer and winter, respectively. Our study explores the linkage between aerosol source and transport path and bacterial composition, which has implication to understanding of land-sea transmission of bacterial taxa.

Microbial community and network responses across strong environmental gradients: How do they compare with macroorganisms?

The way strong environmental gradients shape multispecific assemblages has allowed us to examine a suite of ecological and evolutionary hypotheses about structure, regulation and community responses to fluctuating environments. But whether the highly diverse co-occurring microorganisms are shaped in similar ways as macroscopic organisms across the same gradients has yet to be addressed in most ecosystems. Here, we characterize intertidal biofilm bacteria communities, comparing zonation at both the "species" and community levels, as well as network attributes, with co-occurring macroalgae and invertebrates in the same rocky shore system. The results revealed that the desiccation gradient has a more significant impact on smaller communities, while both desiccation and submersion gradients (surge) affect the larger, macroscopic communities. At the community level, we also confirmed the existence of distinct communities within each intertidal zone for microorganisms, similar to what has been previously described for macroorganisms. But our results indicated that dominant microbial organisms along the same environmental gradient exhibited less differentiation across tidal levels than their macroscopic counterparts. However, despite the substantial differences in richness, size and attributes of co-occurrence networks, both macro- and micro-communities respond to stress gradients, leading to the formation of similar zonation patterns in the intertidal rocky shore.

Salinity-driven ecology and diversity changes of heterocytous cyanobacteria in Australian freshwater and coastal-marine microbial mats

N₂ -fixing heterocytous cyanobacteria are considered to play a minor role in sustaining coastal microbial mat communities developing under normal marine to hypersaline conditions. Here, we investigated microbial mats growing under different salinities from freshwater mats of Giblin River (Tasmania) to metahaline and hypersaline mats of Shark Bay (Western Australia). Analyses of genetic (rRNA and mRNA) and biological markers (heterocyte glycolipids) revealed an unexpectedly large diversity of heterocytous cyanobacteria in all the studied microbial mat communities. It was observed that the taxonomic distribution as well as abundance of cyanobacteria is strongly affected by salinity. Low salinity favoured the presence of heterocytous cyanobacteria in freshwater mats, while mats thriving in higher salinities mainly supported the growth unicellular and filamentous non-heterocytous genera. However, even though mRNA transcripts derived from heterocytous cyanobacteria were lower in Shark Bay (<6%) microbial mats, functional analyses revealed that these diazotrophs were transcribing a substantial proportion of the genes involved in biofilm formation and nitrogen fixation. Overall, our data reveal an unexpectedly high diversity of heterocytous cyanobacteria (e.g. Calothrix, Scytonema, Nodularia, Gloeotrichia, Stigonema, Fischerella and Chlorogloeopsis) that had yet to be described in metahaline and hypersaline microbial mats from Shark Bay and that they play a vital role in sustaining the ecosystem functioning of coastal-marine microbial mat systems.

Bacterial Communities Associated with the Biofilms Formed in High-Altitude Brackish Water Pangong Tso Located in the Himalayan Plateau

Pangong Tso is a long and narrow lake situated at an altitude of ~ 4266 m amsl in the Himalayan Plateau on the side of the India/China border. Biofilm has been observed in a small area near the shore of Pangong Tso. Bacterial communities of the lake sediment, water and biofilms were studied using amplicon sequencing of V3-V4 region of the 16S rRNA gene. The standard QIIME pipeline was used for analysis. The metabolic potential of the community was predicted using functional prediction tool Tax4Fun. Bacterial phyla Proteobacteria, followed by Bacteroidetes, Acidobacteria, Planctomycetes, Actinobacteria, and Firmicutes, were found to be dominant across these samples. Shannon's and Simpson's alpha diversity analysis revealed that sediment communities are the most diverse, and water communities are the least diverse. Principal Coordinates based beta diversity analysis showed significant variation in the bacterial communities of the water, sediment and biofilm samples. Bacterial phyla Verrucomicrobia, Deinococcus-Thermus and Cyanobacteria were explicitly enriched in the biofilm samples. Predictive functional profiling of these bacterial communities showed a higher abundance of genes involved in photosynthesis, biosynthesis of secondary metabolites, carbon fixation in photosynthetic organisms and glyoxylate and dicarboxylate metabolism in the biofilm sample. In conclusion, the Pangong Tso bacterial communities are quite similar to other saline and low-temperature lakes in the Tibetan Plateau. Bacterial community structure of the biofilm samples was significantly different from that of the water and sediment samples and enrichment of saprophytic communities was observed in the biofilm samples, indicating an important succession event in this high-altitude lake.

Global distribution of a chlorophyll f cyanobacterial marker

Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype’s distribution.

Substantial near-infrared radiation-driven photosynthesis of chlorophyll f-containing cyanobacteria in a natural habitat

Far-red absorbing chlorophylls are constitutively present as chlorophyll (Chl) d in the cyanobacterium Acaryochloris marina, or dynamically expressed by synthesis of Chl f, red-shifted phycobiliproteins and minor amounts of Chl d via far-red light photoacclimation in a range of cyanobacteria, which enables them to use near-infrared-radiation (NIR) for oxygenic photosynthesis. While the biochemistry and molecular physiology of Chl f-containing cyanobacteria has been unraveled in culture studies, their ecological significance remains unexplored and no data on their in situ activity exist. With a novel combination of hyperspectral imaging, confocal laser scanning microscopy, and nanoparticle-based O₂ imaging, we demonstrate substantial NIR-driven oxygenic photosynthesis by endolithic, Chl f-containing cyanobacteria within natural beachrock biofilms that are widespread on (sub)tropical coastlines. This indicates an important role of NIR-driven oxygenic photosynthesis in primary production of endolithic and other shaded habitats.

Temperature modulates Fischerella thermalis ecotypes in Porcelana Hot Spring

In the Porcelana Hot Spring (Northern Patagonia), true-branching cyanobacteria are the dominant primary producers in microbial mats, and they are mainly responsible for carbon and nitrogen fixation. However, little is known about their metabolic and genomic adaptations at high temperatures. Therefore, in this study, a total of 81 Fischerella thermalis strains (also known as Mastigocladus laminosus) were isolated from mat samples in a thermal gradient between 61-46°C. The complementary use of proteomic comparisons from these strains, and comparative genomics of F. thermalis pangenomes, suggested that at least two different ecotypes were present within these populations. MALDI-TOF MS analysis separated the strains into three clusters; two with strains obtained from mats within the upper temperature range (61 and 54°C), and a third obtained from mats within the lower temperature range (51 and 46°C). Both groups possessed different but synonymous nifH alleles. The main proteomic differences were associated with the abundance of photosynthesis-related proteins. Three F. thermalis metagenome assembled genomes (MAGs) were described from 66, 58 and 48°C metagenomes. These pangenomes indicated a divergence of orthologous genes and a high abundance of exclusive genes at 66°C. These results improved the current understanding of thermal adaptation of F. thermalis and the evolution of these thermophilic cyanobacterial species.

Cyanobacterial Diversity in Microbial Mats from the Hypersaline Lagoon System of Araruama, Brazil: An In-depth Polyphasic Study

Microbial mats are complex, micro-scale ecosystems that can be found in a wide range of environments. In the top layer of photosynthetic mats from hypersaline environments, a large diversity of cyanobacteria typically predominates. With the aim of strengthening the knowledge on the cyanobacterial diversity present in the coastal lagoon system of Araruama (state of Rio de Janeiro, Brazil), we have characterized three mat samples by means of a polyphasic approach. We have used morphological and molecular data obtained by culture-dependent and -independent methods. Moreover, we have compared different classification methodologies and discussed the outcomes, challenges, and pitfalls of these methods. Overall, we show that Araruama's lagoons harbor a high cyanobacterial diversity. Thirty-six unique morphospecies could be differentiated, which increases by more than 15% the number of morphospecies and genera already reported for the entire Araruama system. Morphology-based data were compared with the 16S rRNA gene phylogeny derived from isolate sequences and environmental sequences obtained by PCR-DGGE and pyrosequencing. Most of the 48 phylotypes could be associated with the observed morphospecies at the order level. More than one third of the sequences demonstrated to be closely affiliated (best BLAST hit results of ≥99%) with cyanobacteria from ecologically similar habitats. Some sequences had no close relatives in the public databases, including one from an isolate, being placed as “loner” sequences within different orders. This hints at hidden cyanobacterial diversity in the mats of the Araruama system, while reinforcing the relevance of using complementary approaches to study cyanobacterial diversity.

Morphological and molecular study of the cyanobiont-bearing dinoflagellate Sinophysis canaliculata from the Canary Islands (eastern central Atlantic)

The presence of the benthic dinophysoid dinoflagellate Sinophysis canaliculata has been reported in the Canary Islands (eastern central Atlantic) in live field observations and on fixed macroalgal samples from intertidal ponds (26 sampling sites from El Hierro, Tenerife, Gran Canaria, Fuerteventura and Lanzarote islands). In vivo Sinophysis cells were typically pale pink colored. Light microscopy and scanning electron microscopy micrographs showed a small characteristic narrow hypothecal cut that matched the original description of S. canaliculata. SSU rRNA gene (rDNA) nuclear phylogeny showed that S. canaliculata is closely related to S. microcephalus. Sinophysis specimens displayed cyanobacterial endosymbionts with orange autofluorescence from phycoerythrins. SSU rDNA analyses of the cyanobionts nearly matched a former sequence obtained from S. canaliculata in the Pacific Ocean (Japan). S. canaliculata survived up to 5 months in the original seawater samples. During that period cyanobionts were always present and maintained their orange autofluorescence, although the pink color gradually vanished (<1 month) in most individuals. Molecular similarity of Sinophysis cyanobionts from the Canary Islands and Japanese waters suggest a deterministic relationship, likely a temporary maintenance inside their host via some specific grazing system.

Chlorophyll f distribution and dynamics in cyanobacterial beachrock biofilms

Chlorophyll (Chl) f, the most far-red (720-740 nm) absorbing Chl species, was discovered in cyanobacterial isolates from stromatolites and subsequently in other habitats as well. However, the spatial distribution and temporal dynamics of Chl f in a natural habitat have so far not been documented. Here, we report the presence of Chl f in cyanobacterial beachrock biofilms. Hyperspectral imaging on cross-sections of beachrock from Heron Island (Great Barrier Reef, Australia), showed a strong and widely distributed signature of Chl f absorption in an endolithic layer below the dense cyanobacterial surface biofilm that could be localized to aggregates of Chroococcidiopsis-like unicellular cyanobacteria packed within a thick common sheath. High-pressure liquid chromatography-based pigment analyses showed in situ ratios of Chl f to Chl a of 5% in brown-pigmented zones of the beachrock, with lower ratios of ~0.5% in the black- and pink-pigmented biofilm zones. Enrichment experiments with black beachrock biofilm showed stimulated synthesis of Chl f and Chl d when grown under near-infrared radiation (NIR; 740 nm), with a Chl f to Chl a ratio increasing 4-fold to 2%, whereas the Chl d to Chl a ratio went from 0% to 0.8%. Enrichments grown under white light (400-700 nm) produced no detectable amounts of either Chl d or Chl f. Beachrock cyanobacteria thus exhibited characteristics of far-red light photoacclimation, enabling Chl f -containing cyanobacteria to thrive in optical niches deprived of visible light when sufficient NIR is prevalent.

Nitrogen fixation in a non-heterocystous cyanobacterial mat from a mountain river

In situ nitrogen fixation was investigated in a cyanobacterial mat growing on the bed of rocks of the Muga River, Spain. The filamentous non-heterocystous cyanobacterium Schizothrix dominated the mat, showing nitrogenase activity in the light at similar rates to those found in nearby heterocystous Rivularia colonies. N2 fixation in the light was significantly increased by an inhibitor of PSII and oxygen evolution, DCMU (3-[3,4-dichlorophenyl]-1,1-dimethylurea), and anaerobic conditions. However, no nitrogenase activity was found in the dark. Addition of fructose as a respiratory substrate induced nitrogenase activity in samples incubated under aerobic conditions in the dark but not in anaerobic conditions. Microelectrode oxygen profiles showed internal microaerobic microzones where nitrogen fixation might concentrate. Analyses of the 16S rRNA gene revealed only the presence of sequences belonging to filamentous non-heterocystous cyanobacteria. nifH gene diversity showed that the major phylotypes also belonged to this group. One of the three strains isolated from the Schizothrix mat was capable of fixing N2 and growing in the absence of combined N. This was consistent with the nifH gene analysis. These results suggest a relevant contribution of non-heterocystous cyanobacteria to nitrogen fixation in these mats.

The cyanobacterium Mastigocladus fulfills the nitrogen demand of a terrestrial hot spring microbial mat

Cyanobacteria from Subsection V (Stigonematales) are important components of microbial mats in non-acidic terrestrial hot springs. Despite their diazotrophic nature (N2 fixers), their impact on the nitrogen cycle in such extreme ecosystems remains unknown. Here, we surveyed the identity and activity of diazotrophic cyanobacteria in the neutral hot spring of Porcelana (Northern Patagonia, Chile) during 2009 and 2011-2013. We used 16S rRNA and the nifH gene to analyze the distribution and diversity of diazotrophic cyanobacteria. Our results demonstrate the dominance of the heterocystous genus Mastigocladus (Stigonematales) along the entire temperature gradient of the hot spring (69-38 °C). In situ nitrogenase activity (acetylene reduction), nitrogen fixation rates (cellular uptake of (15)N2) and nifH transcription levels in the microbial mats showed that nitrogen fixation and nifH mRNA expression were light-dependent. Nitrogen fixation activities were detected at temperatures ranging from 58 °C to 46 °C, with maximum daily rates of 600 nmol C2H4 cm(-2) per day and 94.1 nmol N cm(-2) per day. These activity patterns strongly suggest a heterocystous cyanobacterial origin and reveal a correlation between nitrogenase activity and nifH gene expression during diurnal cycles in thermal microbial mats. N and C fixation in the mats contributed ~3 g N m(-2) per year and 27 g C m(-2) per year, suggesting that these vital demands are fully met by the diazotrophic and photoautotrophic capacities of the cyanobacteria in the Porcelana hot spring.

Influence of local and global environmental parameters on the composition of cyanobacterial mats in a tropical lagoon

Cyanobacteria-dominated microbial mat communities thrive widely and year round in coral reefs and tropical lagoons, with periodic massive development of benthic blooms. We studied the diversity and spatiotemporal variation of the cyanobacterial dominance in mats of the shallow lagoon of La Réunion Island in the Indian Ocean by means of denaturing gradient gel electrophoresis and cloning-sequencing approaches targeting the 16S rRNA gene, combined with macromorphological and micromorphological characterization of corresponding phenotypes. The mat-forming cyanobacteria were highly diversified with at least 67 distinct operational taxonomic units identified in the lagoon, encompassing the entire morphological spectrum of the phylum Cyanobacteria, but with striking dominance of Oscillatoriales and Nostocales. It appeared also that selective pressures acting at different geographical scales have an influence on the structure and composition of these mats dominated by cyanobacteria. First, large changes were observed in their diversity and composition in relation to local changes occurring in their environment. Second, from the data obtained on the richness and composition of the mats and from the comparison with similar studies in the world, tropical mats seem to display wider cyanobacterial richness than in temperate and cold areas. Moreover, these tropical mats share more species with mats in other tropical regions than with those in temperate and cold climatic regions, suggesting that marine cyanobacteria in biofilms and mats display a biogeographic structure.

Phylogeography of cylindrospermopsin and paralytic shellfish toxin-producing nostocales cyanobacteria from mediterranean europe (Spain)

Planktonic Nostocales cyanobacteria represent a challenge for microbiological research because of the wide range of cyanotoxins that they synthesize and their invasive behavior, which is presumably enhanced by global warming. To gain insight into the phylogeography of potentially toxic Nostocales from Mediterranean Europe, 31 strains of Anabaena (Anabaena crassa, A. lemmermannii, A. mendotae, and A. planctonica), Aphanizomenon (Aphanizomenon gracile, A. ovalisporum), and Cylindrospermopsis raciborskii were isolated from 14 freshwater bodies in Spain and polyphasically analyzed for their phylogeography, cyanotoxin production, and the presence of cyanotoxin biosynthesis genes. The potent cytotoxin cylindrospermopsin (CYN) was produced by all 6 Aphanizomenon ovalisporum strains at high levels (5.7 to 9.1 μg CYN mg(-1) [dry weight]) with low variation between strains (1.5 to 3.9-fold) and a marked extracellular release (19 to 41% dissolved CYN) during exponential growth. Paralytic shellfish poisoning (PSP) neurotoxins (saxitoxin, neosaxitoxin, and decarbamoylsaxitoxin) were detected in 2 Aphanizomenon gracile strains, both containing the sxtA gene. This gene was also amplified in non-PSP toxin-producing Aphanizomenon gracile and Aphanizomenon ovalisporum. Phylogenetic analyses supported the species identification and confirmed the high similarity of Spanish Anabaena and Aphanizomenon strains with other European strains. In contrast, Cylindrospermopsis raciborskii from Spain grouped together with American strains and was clearly separate from the rest of the European strains, raising questions about the current assumptions of the phylogeography and spreading routes of C. raciborskii. The present study confirms that the nostocalean genus Aphanizomenon is a major source of CYN and PSP toxins in Europe and demonstrates the presence of the sxtA gene in CYN-producing Aphanizomenon ovalisporum.

Diazotrophy in alluvial meadows of subarctic river systems

There is currently limited understanding of the contribution of biological N₂ fixation (diazotrophy) to the N budget of large river systems. This natural source of N in boreal river systems may partially explain the sustained productivity of river floodplains in Northern Europe where winter fodder was harvested for centuries without fertilizer amendments. In much of the world, anthropogenic pollution and river regulation have nearly eliminated opportunities to study natural processes that shaped early nutrient dynamics of large river systems; however, pristine conditions in northern Fennoscandia allow for the retrospective evaluation of key biochemical processes of historical significance. We investigated biological N₂ fixation (diazotrophy) as a potential source of nitrogen fertility at 71 independent floodplain sites along 10 rivers and conducted seasonal and intensive analyses at a subset of these sites. Biological N₂ fixation occurred in all floodplains, averaged 24.5 kg N ha⁻¹ yr⁻¹ and was down regulated from over 60 kg N ha⁻¹ yr⁻¹ to 0 kg N ha⁻¹ yr⁻¹ by river N pollution. A diversity of N₂-fixing cyanobacteria was found to colonize surface detritus in the floodplains. The data provide evidence for N₂ fixation to be a fundamental source of new N that may have sustained fertility at alluvial sites along subarctic rivers. Such data may have implications for the interpretation of ancient agricultural development and the design of contemporary low-input agroecosystems.

Herbicides induce change in metabolic and genetic diversity of bacterial community from a cold oligotrophic lake

Pristine cold oligotrophic lakes show unique physical and chemical characteristics with permanent fluctuation in temperature and carbon source availability. Incorporation of organic toxic matters to these ecosystems could alter the bacterial community composition. Our goal was to assess the effects of simazine (Sz) and 2,4 dichlorophenoxyacetic acid (2,4-D) upon the metabolic and genetic diversity of the bacterial community in sediment samples from a pristine cold oligotrophic lake. Sediment samples were collected in winter and summer season, and microcosms were prepared using a ration 1:10 (sediments:water). The microcosms were supplemented with 0.1 mM 2,4-D or 0.5 mM Sz and incubated for 20 days at 10 °C. Metabolic diversity was evaluated by using the Biolog Ecoplate™ system and genetic diversity by 16S rDNA amplification followed by denaturing gradient gel electrophoresis analysis. Total bacterial counts and live/dead ratio were determined by epifluorescence microscopy. The control microcosms showed no significant differences (P > 0.05) in both metabolic and genetic diversity between summer and winter samples. On the other hand, the addition of 2,4-D or Sz to microcosms induces statistical significant differences (P < 0.05) in metabolic and genetic diversity showing the prevalence of Actinobacteria group which are usually not detected in the sediments of these non-contaminated lacustrine systems. The obtained results suggest that contaminations of cold pristine lakes with organic toxic compounds of anthropic origin alter their homeostasis by inhibiting specific susceptible bacterial groups. The concomitant increase of usually low representative bacterial groups modifies the bacterial composition commonly found in this pristine lake.

Fluorescent epibiotic microbial community on the carapace of a Bahamian ostracod

Ostracods collected from shallow coral reefs in the Bahamas were found to exhibit blue light-stimulated orange fluorescence at night. Fluorescent spectra revealed the presence of orange fluorescence with a maximum emission at ~595 nm on the carapace of these ostracods, while scanning electron microscopy revealed a morphologically diverse microbial community covering the entire carapace of these ostracods. Pyrosequencing and cyanobacterial-specific 16S rRNA sequencing reveals that this epibiont community is highly diverse and highly variable between individual ostracods. Many species of Cyanobacteria in the orders Oscillatoriales and Chroococcales, as well as other Proteobacteria and diatom chloroplast sequences, were identified using the cyanobacterial-specific primers. While no fluorescent proteins or phycoerythrin were detected in these ostracods, it is possible that the observed orange fluorescence is the result of carotenoid fluorescence from Cyanobacteria. The microbial consortium forms an epibiotic biofilm on the carapace of these ostracods whose functions are unknown.

Epiphytic cyanobacteria of the seagrass Cymodocea rotundata: diversity, diel nifH expression and nitrogenase activity

Seagrasses are photoautotrophic, ecologically important components of many globally widespread coastal ecosystems, in which combined nitrogen may limit their production. We examined the biodiversity and diazotrophic capacity of microbial epiphytes associated with the phyllosphere of the seagrass Cymodocea rotundata of the Western Indian Ocean. Light microscopy, 16S rRNA and nifH gene analysis revealed the dominance of cyanobacteria in the epiphytic microbial community. Most phylotypes were related to free-living uncultured benthic cyanobacteria, while some to cyanobacterial endosymbionts of marine diatoms. Novel and potentially diazotrophic species, some of known pantropical distribution, were also discovered. Significant diel nitrogenase activities (acetylene reduction assay) were recorded (up to 358 ± 232 nmol C2H4 g(-1) of seagrass FW h(-1)). The nifH gene expression patterns showed that heterocystous phylotypes may be the dominant diazotrophs during the day and non-heterocystous at night. These data show that C. rotundata is colonized by diverse diazotrophic cyanobacteria species and suggest that these may be beneficial partners of seagrasses in nitrogen-depleted waters.

Molecular fingerprinting of cyanobacteria from river biofilms as a water quality monitoring tool

Benthic cyanobacterial communities from Guadarrama River (Spain) biofilms were examined using temperature gradient gel electrophoresis (TGGE), comparing the results with microscopic analyses of field-fixed samples and the genetic characterization of cultured isolates from the river. Changes in the structure and composition of cyanobacterial communities and their possible association with eutrophication in the river downstream were studied by examining complex TGGE patterns, band extraction, and subsequent sequencing of 16S rRNA gene fragments. Band profiles differed among sampling sites depending on differences in water quality. The results showed that TGGE band richness decreased in a downstream direction, and there was a clear clustering of phylotypes on the basis of their origins from different locations according to their ecological requirements. Multivariate analyses (cluster analysis and canonical correspondence analysis) corroborated these differences. Results were consistent with those obtained from microscopic observations of field-fixed samples. According to the phylogenetic analysis, morphotypes observed in natural samples were the most common phylotypes in the TGGE sequences. These phylotypes were closely related to Chamaesiphon, Aphanocapsa, Pleurocapsa, Cyanobium, Pseudanabaena, Phormidium, and Leptolyngbya. Differences in the populations in response to environmental variables, principally nutrient concentrations (dissolved inorganic nitrogen and soluble reactive phosphorus), were found. Some phylotypes were associated with low nutrient concentrations and high levels of dissolved oxygen, while other phylotypes were associated with eutrophic-hypertrophic conditions. These results support the view that once a community has been characterized and its genetic fingerprint obtained, this technique could be used for the purpose of monitoring rivers.

High cyanobacterial nifH gene diversity in Arctic seawater and sea ice brine

Although cyanobacterial diazotrophs are common in Arctic terrestrial and freshwater habitats, they have been assumed to be absent from Arctic marine habitats. We report here a high diversity of cyanobacterial nifH genes in Fram Strait and the Greenland Sea. The nifH gene encodes the iron protein of the nitrogenase enzyme complex, which is essential for biological N2 fixation. Using primers specific for nifH genes we uncovered communities of autotrophic and heterotrophic bacteria in sea ice brine and seawater between latitudes 65 and 81°N. Cyanobacteria (Oscillatoriales and Chroococcales) with known marine planktonic and benthic distributions were distinguished, alongside a mix of metabolically versatile eubacteria (nifH Clusters I and III). Using primers selective for cyanobacterial nifH genes we identified filamentous non-heterocystous Trichodesmium-like and LPP (Leptolyngbya, Phormidium and Plectonema)-like Oscillatoriales, as well as Cyanothece-like Chroococcales in a brine sample from 81°N. The occurrence of Trichodesmium-like cyanobacteria was further confirmed by sequences of the hetR gene of Trichodesmium. Microscopic examinations confirmed the presence of viable filamentous and unicellular cyanobacteria. Our results reveal the potential for microbial N2 fixation in the Arctic seas. However, it is still left to determine if these genes are also metabolically active before any biogeochemical importance of diazotrophy in the polar oceans can be assessed.

Culture-dependent characterization of cyanobacterial diversity in the intertidal zones of the Portuguese coast: a polyphasic study

Cyanobacteria are important primary producers, and many are able to fix atmospheric nitrogen playing a key role in the marine environment. However, not much is known about the diversity of cyanobacteria in Portuguese marine waters. This paper describes the diversity of 60 strains isolated from benthic habitats in 9 sites (intertidal zones) on the Portuguese South and West coasts. The strains were characterized by a morphological study (light and electron microscopy) and by a molecular characterization (partial 16S rRNA, nifH, nifK, mcyA, mcyE/ndaF, sxtI genes). The morphological analyses revealed 35 morphotypes (15 genera and 16 species) belonging to 4 cyanobacterial Orders/Subsections. The dominant groups among the isolates were the Oscillatoriales. There is a broad congruence between morphological and molecular assignments. The 16S rRNA gene sequences of 9 strains have less than 97% similarity compared to the sequences in the databases, revealing novel cyanobacterial diversity. Phylogenetic analysis, based on partial 16S rRNA gene sequences showed at least 12 clusters. One-third of the isolates are potential N(2)-fixers, as they exhibit heterocysts or the presence of nif genes was demonstrated by PCR. Additionally, no conventional freshwater toxins genes were detected by PCR screening.

Composition and diversity of nifH genes of nitrogen-fixing cyanobacteria associated with boreal forest feather mosses

Recent studies have revealed that nitrogen fixation by cyanobacteria living in association with feather mosses is a major input of nitrogen to boreal forests. We characterized the community composition and diversity of cyanobacterial nifH phylotypes associated with each of two feather moss species (Pleurozium schreberi and Hylocomium splendens) on each of 30 lake islands varying in ecosystem properties in northern Sweden. Nitrogen fixation was measured using acetylene reduction, and nifH sequences were amplified using general and cyanobacterial selective primers, separated and analyzed using density gradient gel electrophoresis (DGGE) or cloning, and further sequenced for phylogenetic analyses. Analyses of DGGE fingerprinting patterns revealed two host-specific clusters (one for each moss species), and sequence analysis showed five clusters of nifH phylotypes originating from heterocystous cyanobacteria. For H. splendens only, N(2) fixation was related to both nifH composition and diversity among islands. We demonstrated that the cyanobacterial communities associated with feather mosses show a high degree of host specificity. However, phylotype composition and diversity, and nitrogen fixation, did not differ among groups of islands that varied greatly in their availability of resources. These results suggest that moss species identity, but not extrinsic environmental conditions, serves as the primary determinant of nitrogen-fixing cyanobacterial communities that inhabit mosses.

Beachrock formation in temperate coastlines: examples in sand-gravel beaches adjacent to the Nerbioi-Ibaizabal Estuary (Bilbao, Bay of Biscay, North of Spain)

Beachrocks are coastal sedimentary formations resulting from a relative rapid cementation of beach sediments by the precipitation of carbonate cements. These lithified structures are not usually observed at temperate settings. The present work is focused on the occurrence of a significant intertidal cementation in sand-gravel beaches formed among 43°N latitude coastline, close to the Nerbioi-Ibaizabal estuary (Bilbao, Bay of Biscay, North of Spain). Raman micro-spectroscopy combined with SEM-EDX analyses and petrographic descriptions have been applied for the determination of the cement generations and the cemented materials compositions of the beachrock outcrops. In general terms, the cements described were: Cement Generation 1 (CG 1, aragonite, high-magnesium calcite and silicate mixtures), Cement Generation 2 (CG 2, aragonite) and Cement Generation 3 (CG 3, mixtures of CaCO(3) polymorphs and iron oxides). The rest of the interstitial porosity of the rocks appeared either empty or filled with heterogeneous cemented mixtures of previously reworked compounds. The mineralogy, the regular distribution and the isopachous character of the carbonate cements together with the accurate cementation at advanced seaward bands propose a possible marine-phreatic context for the beachrock formation. However, the impure cements and the materials covering the interstitial porosity seem to be the result of both, the weathering actions consequences and the surface alterations of specific grains. Moreover, the presence of modern cemented materials (e.g. slag, bricks and pebbles) suggest a recent formation of the phenomenon.

The dynamics of microbial partnerships in the coral Isopora palifera

Both bacteria and algal symbionts (genus Symbiodinium), the two major microbial partners in the coral holobiont, respond to fluctuations in the environment, according to current reports; however, little evidence yet indicates that both populations have any direct interaction with each other in seasonal fluctuation. In this study, we present field observations of a compositional change in bacteria and Symbiodinium in the coral Isopora palifera in three separate coral colonies following monthly sampling from February to November in 2008. Using massively parallel pyrosequencing, over 200,000 bacterial V6 sequences were classified to build the bacterial community profile; in addition, the relative composition and quantity of Symbiodinium clades C and D were determined by real-time PCR. The results showed that coral-associated bacterial and Symbiodinium communities were highly dynamic and dissimilar among the tagged coral colonies, suggesting that the effect of host specificity was insignificant. The coral-associated bacterial community was more diverse (Shannon index up to 6.71) than previous estimates in other corals and showed rapid seasonal changes. The population ratios between clade C and D groups of Symbiodinium varied in the tagged coral colonies through the different seasons; clade D dominated in most of the samples. Although significant association between bacteria and symbiont was not detected, this study presents a more detailed picture of changes in these two major microbial associates of the coral at the same time, using the latest molecular approaches.

Isolation of novel extreme-tolerant cyanobacteria from a rock-dwelling microbial community by using exposure to low Earth orbit

Many cyanobacteria are known to tolerate environmental extremes. Motivated by an interest in selecting cyanobacteria for applications in space, we launched rocks from a limestone cliff in Beer, Devon, United Kingdom, containing an epilithic and endolithic rock-dwelling community of cyanobacteria into low Earth orbit (LEO) at a height of approximately 300 kilometers. The community was exposed for 10 days to isolate cyanobacteria that can survive exposure to the extreme radiation and desiccating conditions associated with space. Culture-independent (16S rRNA) and culture-dependent methods showed that the cyanobacterial community was composed of Pleurocapsales, Oscillatoriales, and Chroococcales. A single cyanobacterium, a previously uncharacterized extremophile, was isolated after exposure to LEO. We were able to isolate the cyanobacterium from the limestone cliff after exposing the rock-dwelling community to desiccation and vacuum (0.7 x 10(-3) kPa) in the laboratory. The ability of the organism to survive the conditions in space may be linked to the formation of dense colonies. These experiments show how extreme environmental conditions, including space, can be used to select for novel microorganisms. Furthermore, it improves our knowledge of environmental tolerances of extremophilic rock-dwelling cyanobacteria.

Analysis of a diverse assemblage of diazotrophic bacteria from Spartina alterniflora using DGGE and clone library screening

Methods to assess the diversity of the diazotroph assemblage in the rhizosphere of the salt marsh cordgrass, Spartina alterniflora were examined. The effectiveness of nifH PCR-denaturing gradient gel electrophoresis (DGGE) was compared to that of nifH clone library analysis. Seventeen DGGE gel bands were sequenced and yielded 58 nonidentical nifH sequences from a total of 67 sequences determined. A clone library constructed using the GC-clamp nifH primers that were employed in the PCR-DGGE (designated the GC-Library) yielded 83 nonidentical sequences from a total of 257 nifH sequences. A second library constructed using an alternate set of nifH primers (N-Library) yielded 83 nonidentical sequences from a total of 138 nifH sequences. Rarefaction curves for the libraries did not reach saturation, although the GC-Library curve was substantially dampened and appeared to be closer to saturation than the N-Library curve. Phylogenetic analyses showed that DGGE gel band sequencing recovered nifH sequences that were frequently sampled in the GC-Library, as well as sequences that were infrequently sampled, and provided a species composition assessment that was robust, efficient, and relatively inexpensive to obtain. Further, the DGGE method permits a large number of samples to be examined for differences in banding patterns, after which bands of interest can be sampled for sequence determination.