Community phylogenetic diversity of cyanobacterial mats associated with geothermal springs along a tropical intertidal gradient

Coaggregation Occurs between a Piliated Unicellular Cyanobacterium, Thermosynechococcus, and a Filamentous Bacterium, Chloroflexus aggregans

Cyanobacteria are widely distributed in natural environments including geothermal areas. A unicellular cyanobacterium, Thermosynechococcus, in a deeply branching lineage, develops thick microbial mats with other bacteria, such as filamentous anoxygenic photosynthetic bacteria in the genus Chloroflexus, in slightly alkaline hot-spring water at ~55 °C. However, Thermosynechococcus strains do not form cell aggregates under axenic conditions, and the cells are dispersed well in the culture. In this study, Thermosynechococcus sp. NK55a and Chloroflexus aggregans NBF, isolated from Nakabusa Hot Springs (Nagano, Japan), were mixed in an inorganic medium and incubated at 50 °C under incandescent light. Small cell aggregates were detected after 4 h incubation, the size of cell aggregates increased, and densely packed cell aggregates (100-200 µm in diameter) developed. Scanning electron microscopy analysis of cell aggregates found that C. aggregans filaments were connected with Thermosynechococcus sp. cells via pili-like fibers. Co-cultivation of C. aggregans with a pili-less mutant of Thermosynechococcus sp. did not form tight cell aggregates. Cell aggregate formation was observed under illumination with 740 nm LED, which was utilized only by C. aggregans. These results suggested that Chloroflexus filaments gather together via gliding motility, and piliated cyanobacterial cells cross-link filamentous cells to form densely packed cell aggregates.

Community structure of thermophilic photosynthetic microbial mats and flocs at Sembawang Hot Spring, Singapore

The Sembawang Hot Spring in Singapore lies at the foot of a major regional geological feature called the Bentong-Raub Suture Zone. Amid an extensively managed surface geothermal park, an undisturbed hot spring emerges with source water at 61°C, pH 6.8, and 1 mg/L dissolved sulfide. A small main pool at the source supported orange-green benthic flocs, whereas the outflow channel with gradually less extreme environmental stress supported extensive vivid green microbial mats. Microscopy revealed that cyanobacterial morphotypes were distinct in flocs and mats at several intervals along the environmental gradient, and we describe a spiraling pattern in the oscillatorian cyanobacteria that may reflect response to poly-extreme stress. Estimation of diversity using 16S rRNA gene sequencing revealed assemblages that were dominated by phototrophic bacteria. The most abundant taxa in flocs at 61°C/1 mg/L sulfide were Roseiflexus sp. and Thermosynechococcus elongatus, whilst the mats at 45.7-55.3°C/0-0.5 mg/L sulfide were dominated by Oscillatoriales cyanobacterium MTP1 and Chloroflexus sp. Occurrence of diverse chemoautotrophs and heterotrophs reflected known thermal ranges for taxa, and of note was the high abundance of thermophilic cellulolytic bacteria that likely reflected the large allochthonous leaf input. A clear shift in ASV-defined putative ecotypes occurred along the environmental stress gradient of the hot spring and overall diversity was inversely correlated to environmental stress. Significant correlations for abiotic variables with observed biotic diversity were identified for temperature, sulfide, and carbonate. A network analysis revealed three putative modules of biotic interactions that also reflected the taxonomic composition at intervals along the environmental gradient. Overall, the data indicated that three distinct microbial communities were supported within a small spatial scale along the poly-extreme environmental gradient. The findings add to the growing inventory of hot spring microbiomes and address an important biogeographic knowledge gap for the region.

Radiation-Tolerant Bacteria Isolated from High Altitude Soil in Tibet

This study reports the identification of ionising radiation tolerant bacteria from a high elevation arid region of central Tibet. Nineteen isolates were isolated from soil exposed to ionising radiation at doses from 0 to 15 kGy. Isolates were phylogenetically characterised using 16S rRNA gene sequences. Most isolates comprised taxa from the Actinobacteria, Cyanobacteria, Firmicutes and proteobacteria and these survived doses up to 5 kGy. The Firmicutes and Deinococci also survived doses up to 10 kGy, and the highest dose of 15 kGy was survived only by the Deinococci. No altitude-related pattern was discernible within the range 4638-5240 m, instead culturable bacterial estimates for irradiated soil were strongly influenced by the abundance of Deinococci. We conclude that the relatively high UV exposure in Tibet has contributed to the high diversity of radiation tolerant soil bacteria. In addition, the strong association between desiccation-tolerance and radiation tolerance pathways suggests the arid environment may also have selected in favour of radiation tolerant taxa.

The molecular dimension of microbial species: 1. Ecological distinctions among, and homogeneity within, putative ecotypes of Synechococcus inhabiting the cyanobacterial mat of Mushroom Spring, Yellowstone National Park

Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over a large number of habitat types in the Mushroom Spring microbial mat. Putative ecological species [putative ecotypes (PEs)], which were predicted by an evolutionary simulation based on the Stable Ecotype Model (Ecotype Simulation), exhibited distinct distributions relative to temperature-defined positions in the effluent channel and vertical position in the upper 1 mm-thick mat layer. Importantly, in most cases variants predicted to belong to the same PE formed unique clusters relative to temperature and depth in the mat in canonical correspondence analysis, supporting the hypothesis that while the PEs are ecologically distinct, the members of each ecotype are ecologically homogeneous. PEs responded differently to experimental perturbations of temperature and light, but the genetic variation within each PE was maintained as the relative abundances of PEs changed, further indicating that each population responded as a set of ecologically interchangeable individuals. Compared to PEs that predominate deeper within the mat photic zone, the timing of transcript abundances for selected genes differed for PEs that predominate in microenvironments closer to upper surface of the mat with spatiotemporal differences in light and O2 concentration. All of these findings are consistent with the hypotheses that Synechococcus species in hot spring mats are sets of ecologically interchangeable individuals that are differently adapted, that these adaptations control their distributions, and that the resulting distributions constrain the activities of the species in space and time.

Microbial community analysis of a coastal hot spring in Kagoshima, Japan, using molecular- and culture-based approaches

Ibusuki hot spring is located on the coastline of Kagoshima Bay, Japan. The hot spring water is characterized by high salinity, high temperature, and neutral pH. The hot spring is covered by the sea during high tide, which leads to severe fluctuations in several environmental variables. A combination of molecular- and culture-based techniques was used to determine the bacterial and archaeal diversity of the hot spring. A total of 48 thermophilic bacterial strains were isolated from two sites (Site 1: 55.6°C; Site 2: 83.1°C) and they were categorized into six groups based on their 16S rRNA gene sequence similarity. Two groups (including 32 isolates) demonstrated low sequence similarity with published species, suggesting that they might represent novel taxa. The 148 clones from the Site 1 bacterial library included 76 operational taxonomy units (OTUs; 97% threshold), while 132 clones from the Site 2 bacterial library included 31 OTUs. Proteobacteria, Bacteroidetes, and Firmicutes were frequently detected in both clone libraries. The clones were related to thermophilic, mesophilic and psychrophilic bacteria. Approximately half of the sequences in bacterial clone libraries shared <92% sequence similarity with their closest sequences in a public database, suggesting that the Ibusuki hot spring may harbor a unique and novel bacterial community. By contrast, 77 clones from the Site 2 archaeal library contained only three OTUs, most of which were affiliated with Thaumarchaeota.

Vertical partitioning and expression of primary metabolic genes in a thermophilic microbial mat

A thermophilic microbial mat with a relatively simple morphological composition was used to study the expression of key metabolic genes between mat layers. Mats comprised Roseiflexus castenholzii, Synechococcus sp., a Sphingomonas-like proteobacterial taxon and an unidentified member of the Thermotogae as determined by 16S rRNA phylotypes. The diversity of expressed loci for key genes involved in oxygenic photosynthesis (cbbL), anoxygenic photosynthesis (pufM) and nitrogen fixation (nifH) was assessed. The cyanobacterial surface layer supported two cbbL transcripts, with closest phylogenetic affinity to those from the cyanobacterium Synechococcus sp. and a proteobacterium Nitrobacter sp. This indicates that both photoautotrophic and chemolithoautotrophic carbon dioxide fixation may occur in this mat layer. Lower layers did not support cbbL transcripts. Anoxygenic photosynthesis was indicated by a single pufM transcript with closest affinity to that of R. castenholzii. Expression occurred in all layers beneath the cyanobacterial surface layer. Expression of a single nifH transcript with closest affinity to a proteobacterial nitrogenase occurred in samples throughout all mat layers.

Bacterial community composition in thermophilic microbial mats from five hot springs in central Tibet

Despite detailed study of selected thermophilic taxa, overall community diversity of bacteria in thermophilic mats remains relatively poorly understood. A sequence-based survey of bacterial communities from several hot spring locations in central Tibet was undertaken. Diversity and frequency of occurrence for 140 unique 16S rRNA gene phylotypes were identified in clone libraries constructed from environmental samples. A lineage-per-time plot revealed that individual locations have evolved to support relatively large numbers of phylogenetically closely related phylotypes. Application of the F ( ST ) statistic and P test to community data was used to demonstrate that phylogenetic divergence between locations was significant, thus emphasizing the status of hot springs as isolated habitats. Among phylotypes, only the Chlorobi were ubiquitous to all mats, other phototrophs (Cyanobacteria and Chloroflexi) occurred in most but not all samples and generally accounted for a large number of recovered phylotypes. Phylogenetic analyses of phototrophic phylotypes revealed support for location-specific lineages. The alpha, beta and gamma proteobacteria were also frequently recovered phyla, suggesting they may be abundant phylotypes in mats, a hitherto unappreciated aspect of thermophilic mat biodiversity. Samples from one location indicated that where phototrophic bacteria were rare or absent due to niche disturbance, the relative frequency of proteobacterial phylotypes increased.

Rapid adaptation of phytoplankters to geothermal waters is achieved by single mutations: were extreme environments 'Noah's Arks' for photosynthesizers during the Neoproterozoic 'snowball Earth'?

Geothermal waters often support remarkable communities of microalgae and cyanobacteria apparently living at the extreme limits of their tolerance. Little is known about the mechanisms allowing adaptation of mesophilic phytoplankters to such extreme conditions, but recent studies are challenging many preconceived notions about this. The aim of this study was to analyse mechanisms allowing adaptation of mesophilic microalgae and cyanobacteria to stressful geothermal waters. To distinguish between the pre-selective or post-selective origin of adaptation processes allowing the proliferation of mesophilic phytoplankters in geothermal waters, several Luria-Delbrück fluctuation analysis were performed with the microalga Dictyosphaerium chlorelloides and the cyanobacterium Microcystis aeruginosa, both isolated from nonextreme waters. Geothermal waters from seven places in Italy and five icebound places at Los Andes in Argentina were used as selective agents. Physiological adaptation was achieved in the least toxic waters. In contrast, rapid genetic adaptation was observed in waters ostensibly lethal for the experimental organisms. This adaptation was achieved as consequence of single mutations at one locus. It was hypothesized that a similar mechanism of rapid genetic adaptation could explain the survival of photosynthetic life during the Neoproterozoic 'snowball Earth,' where geothermal refuges such as those studied could have been 'Noah's Arks' for microalgae and cyanobacteria.

Early colonization of thermal niches in a silica-depositing hot spring in central Tibet

Thermophilic microbial mats dominated by the anoxygenic phototroph Roseiflexus castenholzii commonly develop around sinter-depositing geysers in the Daggyai Tso geothermal field of central Tibet. In this study we used morphological and molecular genetic techniques to reveal a diverse pioneer biofilm community including both archaea and bacteria involved in early colonization of such thermal niches at temperatures ranging from 46 to 77 degrees C. Sinter precipitation and biomineralization were evident at all locations, but the latter was selective between taxa and most evident on filamentous cells. Evidence for possible indirect biosignatures from biofilms overwhelmed by sinter deposition was found. Succession to a mature community appeared to relate to the growth rate for key taxa outpacing that of silicification within an optimum temperature range of 54-61 degrees C. The thin surface layer of silicification-resistant cyanobacteria that developed on the surface of mature mats may play a role in preventing biomineralization of the susceptible R. castenholzii beneath within these communities.

Identification and characterization of thermophilicSynechococcusspp. isolates from Asian geothermal springs

Two thermophilic cyanobacterial strains, Ts and Bs, collected from Asian geothermal springs were identified morphologically and phylogenetically as Synechococcus in the order Chroococcales and were isolated into axenic cultures. In addition to the high similarities between their full 16S rRNA gene sequences, both strains also shared similar pigment profiles and fatty acid compositions but with varied ratios. Strain Ts had elevated levels of photoprotective pigments such as carotenoid and scytonemin even after prolonged culture under identical laboratory conditions, whereas strain Bs produced more chlorophyll a per unit cell volume, perhaps resulting from UV adaptation in the natural habitats. In addition, strain Ts had more content than strain Bs in terms of the total fatty acids and the proportion of unsaturated fatty acids. Neither isolate was able to fix nitrogen, and they had zero susceptibility to ampicillin and streptomycin.