The microbial composition of three limnologically disparate hypersaline Antarctic lakes

16S rRNA clone library analysis was used to examine the biodiversity and community structure within the sediments of three hypersaline Antarctic lakes. Compared to sediment of low to moderate salinity Antarctic lakes the species richness of the hypersaline lake sediments was 2-20 times lower. The community of Deep Lake (32% salinity, average sediment temperature -15 degrees C) was made up almost entirely of halophilic Archaea. The sediment communities of two meromictic hypersaline lakes, Organic Lake (20% salinity, -7 degrees C) and Ekho Lake (15% salinity, 15 degrees C) were more complex, containing phylotypes clustering within the Proteobacteria and Cytophagales divisions and with algal chloroplasts. Many phylotypes of these lakes were related to taxa more adapted to marine-like salinity and perhaps derive from bacteria exported into the sediment from the lower salinity surface waters. The Ekho Lake clone library contained several major phylotypes related to the Haloanaerobiales, the growth of which appears to be promoted by the comparatively high in situ temperature of this lake.     

Do Patterns of Bacterial Diversity along Salinity Gradients Differ from Those Observed for Macroorganisms?

It is widely accepted that biodiversity is lower in more extreme environments. In this study, we sought to determine whether this trend, well documented for macroorganisms, also holds at the microbial level for bacteria. We used denaturing gradient gel electrophoresis (DGGE) with phylum-specific primers to quantify the taxon richness (i.e., the DGGE band numbers) of the bacterioplankton communities of 32 pristine Tibetan lakes that represent a broad salinity range (freshwater to hypersaline). For the lakes investigated, salinity was found to be the environmental variable with the strongest influence on the bacterial community composition. We found that the bacterial taxon richness in freshwater habitats increased with increasing salinity up to a value of 1‰. In saline systems (systems with >1‰ salinity), the expected decrease of taxon richness along a gradient of further increasing salinity was not observed. These patterns were consistently observed for two sets of samples taken in two different years. A comparison of 16S rRNA gene clone libraries revealed that the bacterial community of the lake with the highest salinity was characterized by a higher recent accelerated diversification than the community of a freshwater lake, whereas the phylogenetic diversity in the hypersaline lake was lower than that in the freshwater lake. These results suggest that different evolutionary forces may act on bacterial populations in freshwater and hypersaline lakes on the Tibetan Plateau, potentially resulting in different community structures and diversity patterns.     

青藏高原淡水湖普莫雍错和盐水湖阿翁错湖底沉积物中细菌群落的垂直分布

【目的】湖泊沉积物中存储着大量独特的微生物,这些微生物在湖泊生态系统生物地球化学循环中扮演着非常重要的角色。然而,很少有研究报道微生物群落在湖泊沉积物中的垂直分布。本文比较研究青藏高原淡水湖普莫雍错和盐水湖阿翁错沉积物在不同深度下细菌的丰度和群落结构。【方法】利用定量PCR(q PCR)和变性梯度凝胶电泳(DGGE)技术分别测定细菌群落的丰度与群落结构。【结果】定量PCR结果显示,湖泊沉积物中细菌丰度均随深度增加而降低,盐水湖阿翁错和淡水湖普莫雍错的细菌丰度分别从1011数量级降到108数量级,从1012数量级降到1010数量级。在相对应的沉积物层,淡水湖沉积物的细菌丰度比盐水湖高1-2个数量级。变性梯度凝胶电泳(DGGE)指纹图谱的分析表明,淡水湖沉积物细菌群落的DGGE条带数(丰富度)显著高于盐水湖(P=0.014);淡水与盐水湖泊沉积物细菌群落结构明显不同,同时在同一湖泊沉积物中上层(0-6 cm)和下层(7-20 cm)细菌群落结构也呈明显分异。系统发育分析表明,盐水湖阿翁错沉积物特有菌门为Gamma-变形菌、拟杆菌门、蓝细菌和栖热菌门,而淡水湖普莫雍错沉积物中特有菌门为Delta-和Beta-变形菌、酸杆菌和绿弯菌门。【结论】青藏高原淡水与盐水湖泊沉积物细菌丰度与群落结构具有明显的差异;同时,细菌群落结构在沉积物的不同深度也表现出差异。这些结果可为进一步阐明青藏高原湖泊生态系统中微生物对气候环境变化的响应提供科学依据。     

Microbial Community Response to Seawater Amendment in Low-Salinity Tidal Sediments

Rising sea levels and excessive water withdrawals upstream are making previously freshwater coastal ecosystems saline. Plant and animal responses to variation in the freshwater–saline interface have been well studied in the coastal zone; however, microbial community structure and functional response to seawater intrusion remains relatively unexplored. Here, we used molecular approaches to evaluate the response of the prokaryotic community to controlled changes in porewater salinity levels in freshwater sediments from the Altamaha River, Georgia, USA. This work is a companion to a previously published study describing results from an experiment using laboratory flow-through sediment core bioreactors to document biogeochemical changes as porewater salinity was increased from 0 to 10 over 35 days. As reported in Weston et al. (Biogeochemistry, 77:375–408, 62), porewater chemistry was monitored, and cores were sacrificed at 0, 9, 15, and 35 days, at which time we completed terminal restriction fragment length polymorphism and 16S rRNA clone library analyses of sediment microbial communities. The biogeochemical study documented changes in mineralization pathways in response to artificial seawater additions, with a decline in methanogenesis, a transient increase in iron reduction, and finally a dominance of sulfate reduction. Here, we report that, despite these dramatic and significant changes in microbial activity at the biogeochemical level, no significant differences were found between microbial community composition of control vs. seawater-amended treatments for either Bacterial or Archaeal members. Further, taxa in the seawater-amended treatment community did not become more “marine-like” through time. Our experiment suggests that, as seawater intrudes into freshwater sediments, observed changes in metabolic activity and carbon mineralization on the time scale of weeks are driven more by shifts in gene expression and regulation than by changes in the composition of the microbial community.     

Phylogenetic diversities and community structure of members of the extremely halophilic Archaea (order Halobacteriales) in multiple saline sediment habitats

We investigated the phylogenetic diversity and community structure of members of the halophilic Archaea (order Halobacteriales) in five distinct sediment habitats that experience various levels of salinity and salinity fluctuations (sediments from Great Salt Plains and Zodletone Spring in Oklahoma, mangrove tree sediments in Puerto Rico, sediment underneath salt heaps in a salt-processing plant, and sediments from the Great Salt Lake northern arm) using Halobacteriales-specific 16S rRNA gene primers. Extremely diverse Halobacteriales communities were encountered in all habitats, with 27 (Zodletone) to 37 (mangrove) different genera identified per sample, out of the currently described 38 Halobacteriales genera. With the exception of Zodletone Spring, where the prevalent geochemical conditions are extremely inhospitable to Halobacteriales survival, habitats with fluctuating salinity levels were more diverse than permanently saline habitats. Sequences affiliated with the recently described genera Halogranum, Halolamina, Haloplanus, Halosarcina, and Halorientalis, in addition to the genera Halorubrum, Haloferax, and Halobacterium, were among the most abundant and ubiquitous genera, suggesting a wide distribution of these poorly studied genera in saline sediments. The Halobacteriales sediment communities analyzed in this study were more diverse than and completely distinct from communities from typical hypersaline water bodies. Finally, sequences unaffiliated with currently described genera represented a small fraction of the total Halobacteriales communities, ranging between 2.5% (Zodletone) to 7.0% (mangrove and Great Salt Lake). However, these novel sequences were characterized by remarkably high levels of alpha and beta diversities, suggesting the presence of an enormous, yet-untapped supply of novel Halobacteriales genera within the rare biosphere of various saline ecosystems.     

新疆天山北坡不同盐湖微生物菌群结构及其影响因子

新疆分布的众多湖泊由于干旱气候成盐作用强烈,近半数已演化到盐湖发展阶段,不同盐湖中也因此蕴含着丰富的耐盐及嗜盐微生物资源。为更好的掌握新疆盐湖微生物资源分布规律及对环境因子变化的响应规律,利用高通量测序技术对新疆天山北坡5个不同演化阶段盐湖湖底沉积物中细菌、古菌多样性和菌群结构及其主要驱动因子进行研究,探讨盐湖演化过程中原核微生物群落结构变化规律。分别采集5个盐湖湖底沉积物样本,进行理化因子测试与细菌和古菌16S rRNA扩增子测序分析,比较不同盐湖理化性质和原核微生物菌群差异,并对原核微生物丰度与环境因子进行关联分析。实验结果表明：5个盐湖湖底沉积物总盐和Na⁺含量顺序为：巴里坤湖 > 伊吾湖 > 艾比湖 > 盐湖 > 柴窝堡湖,除艾比湖外其他四个盐湖沉积物均呈碱性。Alpha多样性结果显示5个盐湖细菌richness、chao1、ACE和shannon丰富度指数均大于古菌相应丰富度指数,不同盐湖细菌丰富度指数差异较大,古菌丰富度指数差异相对较小。从5个盐湖湖底沉积物中共检测获得细菌58门、68纲、138目、253科和560属,古菌4门、8纲、12目、21科和60属,细菌以变形菌门为主,古菌以广古菌门为主。不同盐湖细菌和古菌优势属种类均不相同,巴里坤湖主要是一些嗜盐和耐盐细菌属,而伊吾湖主要是嗜盐和耐盐古菌属,PCoA分析结果也表明不同盐湖微生物在OTUs水平有其独特菌群结构类型。RDA和Bioenv分析结果表明,盐湖湖底沉积物中微生物菌群群落结构主要受Na⁺和总盐（TS）浓度的影响,对细菌菌群结构影响较大,而古菌菌群结构可能受多种理化因子共同调节。此外,盐湖特殊卤水成分会对微生物群落结构产生重大影响。     

Resistance and resilience of benthic biofilm communities from a temperate saltmarsh to desiccation and rewetting

Periods of desiccation and rewetting are regular, yet stressful events encountered by saltmarsh microbial communities. To examine the resistance and resilience of microbial biofilms to such stresses, sediments from saltmarsh creeks were allowed to desiccate for 23 days, followed by rewetting for 4 days, whereas control sediments were maintained under a natural tidal cycle. In the top 2 mm of the dry sediments, salinity increased steadily from 36 to 231 over 23 days, and returned to seawater salinity on rewetting. After 3 days, desiccated sediments had a lower chlorophyll a (Chl a) fluorescence signal as benthic diatoms ceased to migrate to the surface, with a recovery in cell migration and Chl a fluorescence on rewetting. Extracellular β-glucosidase and aminopeptidase activities decreased within the first week of drying, but increased sharply on rewetting. The bacterial community in the desiccating sediment changed significantly from the controls after 14 days of desiccation (salinity 144). Rewetting did not cause a return to the original community composition, but led to a further change. Pyrosequencing analysis of 16S rRNA genes amplified from the sediment revealed diverse microbial responses, for example desiccation enabled haloversatile Marinobacter species to increase their relative abundance, and thus take advantage of rewetting to grow rapidly and dominate the community. A temporal sequence of effects of desiccation and rewetting were thus observed, but the most notable feature was the overall resistance and resilience of the microbial community.     

Substrate type determines metagenomic profiles from diverse chemical habitats

Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance.     

Abundance, distribution, and activity of Fe(II)-oxidizing and Fe(III)-reducing microorganisms in hypersaline sediments of Lake Kasin, southern Russia

The extreme osmotic conditions prevailing in hypersaline environments result in decreasing metabolic diversity with increasing salinity. Various microbial metabolisms have been shown to occur even at high salinity, including photosynthesis as well as sulfate and nitrate reduction. However, information about anaerobic microbial iron metabolism in hypersaline environments is scarce. We studied the phylogenetic diversity, distribution, and metabolic activity of iron(II)-oxidizing and iron(III)-reducing Bacteria and Archaea in pH-neutral, iron-rich salt lake sediments (Lake Kasin, southern Russia; salinity, 348.6 g liter(-1)) using a combination of culture-dependent and -independent techniques. 16S rRNA gene clone libraries for Bacteria and Archaea revealed a microbial community composition typical for hypersaline sediments. Most-probable-number counts confirmed the presence of 4.26 × 10(2) to 8.32 × 10(3) iron(II)-oxidizing Bacteria and 4.16 × 10(2) to 2.13 × 10(3) iron(III)-reducing microorganisms per gram dry sediment. Microbial iron(III) reduction was detected in the presence of 5 M NaCl, extending the natural habitat boundaries for this important microbial process. Quantitative real-time PCR showed that 16S rRNA gene copy numbers of total Bacteria, total Archaea, and species dominating the iron(III)-reducing enrichment cultures (relatives of Halobaculum gomorrense, Desulfosporosinus lacus, and members of the Bacilli) were highest in an iron oxide-rich sediment layer. Combined with the presented geochemical and mineralogical data, our findings suggest the presence of an active microbial iron cycle at salt concentrations close to the solubility limit of NaCl.     

Microbial diversity in water and sediment of Lake Chaka, an athalassohaline lake in northwestern China

We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10(8) cells/g at the water-sediment interface to 10(7) cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.     

Stratification of archaea in the deep sediments of a freshwater meromictic lake: vertical shift from methanogenic to uncultured archaeal lineages

As for lineages of known methanogens, several lineages of uncultured archaea were recurrently retrieved in freshwater sediments. However, knowledge is missing about how these lineages might be affected and structured according to depth. In the present study, the vertical changes of archaeal communities were characterized in the deep sediment of the freshwater meromictic Lake Pavin. For that purpose, an integrated molecular approach was performed to gain information on the structure, composition, abundance and vertical stratification of archaeal communities thriving in anoxic freshwater sediments along a gradient of sediments encompassing 130 years of sedimentation. Huge changes occurred in the structure and composition of archaeal assemblages along the sediment core. Methanogenic taxa (i.e. Methanosaeta and Methanomicrobiales) were progressively replaced by uncultured archaeal lineages (i.e. Marine Benthic Group-D (MBG-D) and Miscellaneous Crenarchaeal Group (MCG)) which are suspected to be involved in the methane cycle.     

Zonation of Microbial Communities by a Hydrothermal Mound in the Atlantis II Deep (the Red Sea)

In deep-sea geothermal rift zones, the dispersal of hydrothermal fluids of moderately-high temperatures typically forms subseafloor mounds. Major mineral components of the crust covering the mound are barite and metal sulfides. As a result of the continental rifting along the Red Sea, metalliferous sediments accumulate on the seafloor of the Atlantis II Deep. In the present study, a barite crust was identified in a sediment core from the Atlantis II Deep, indicating the formation of a hydrothermal mound at the sampling site. Here, we examined how such a dense barite crust could affect the local environment and the distribution of microbial inhabitants. Our results demonstrate distinctive features of mineral components and microbial communities in the sediment layers separated by the barite crust. Within the mound, archaea accounted for 65% of the community. In contrast, the sediments above the barite boundary were overwhelmed by bacteria. The composition of microbial communities under the mound was similar to that in the sediments of the nearby Discovery Deep and marine cold seeps. This work reveals the zonation of microbial communities after the formation of the hydrothermal mound in the subsurface sediments of the rift basin.     

Organic Matter Preservation and Microbial Community Accumulations in Deep-Hypersaline Anoxic Basins

The Eastern Mediterranean Sea hosts several deep hypersaline anoxic basins (DHABs) such as the Bannock, L'Atalante, Discovery, and Urania which, due to strong salinity gradients, have a limited exchange with the overlying seawater. In the present study, a series of environmental variables associated with the origin and quality of organic matter were thoroughly investigated in an attempt to understand the function of these unique ecosystems. The redox potential of sediments collected from the brines as well as from reference sites varied from ?136 to 543 mV and salinity varied from 38 to 380 psu. Principal component analysis of chemical characteristics, including salinity, redox potential, organic carbon and nitrogen content, and C/N ratio grouped the sediments into two major clusters according to their redox state. Aliphatic hydrocarbon analysis revealed that the organic matter in the DHABs was predominantly of terrestrial origin but there was also evidence for petroleum inputs and for organic matter of phototrophic origin. Phospholipid linked fatty acids (PLFA) which were employed to assess the composition of microbial communities were found in greater abundance in stations situated inside the anoxic basins providing also strong evidence for the presence of methanotrophs and sulfate reducers. These results may represent an enhanced preservation of organic matter and an accumulation of microorganisms in these extreme environments. Heterogeneity in microbial community fatty acid profiles was documented between the anoxic sediments and the oxic and suboxic stations. However there were no significant correlations between PLFA and organic matter parameters. Redox conditions appear to influence microbial community composition, highlighting the role of the redox state as a regulator of organic matter preservation and microbial community accumulations in these ancient hypersaline anoxic lakes.     

Microbial Diversity in Water and Sediment of Lake Chaka, an Athalassohaline Lake in Northwestern China

We employed culture-dependent and -independent techniques to study microbial diversity in Lake Chaka, a unique hypersaline lake (32.5% salinity) in northwest China. It is situated at 3,214 m above sea level in a dry climate. The average water depth is 2 to 3 cm. Halophilic isolates were obtained from the lake water, and halotolerant isolates were obtained from the shallow sediment. The isolates exhibited resistance to UV and gamma radiation. Microbial abundance in the sediments ranged from 10⁸ cells/g at the water-sediment interface to 10⁷ cells/g at a sediment depth of 42 cm. A major change in the bacterial community composition was observed across the interface. In the lake water, clone sequences affiliated with the Bacteroidetes were the most abundant, whereas in the sediments, sequences related to low G+C gram-positive bacteria were predominant. A similar change was also present in the archaeal community. While all archaeal clone sequences in the lake water belonged to the Halobacteriales, the majority of the sequences in the sediments were related to those previously obtained from methanogenic soils and sediments. The observed changes in the microbial community structure across the water-sediment interface were correlated with a decrease in salinity from the lake water (32.5%) to the sediments (approximately 4%). Across the interface, the redox state also changed from oxic to anoxic and may also have contributed to the observed shift in the microbial community.     

Microbial diversity and complexity in hypersaline environments: A preliminary assessment

The microbial communities in solar salterns and a soda lake have been characterized using two techniques: BIOLOG, to estimate the metabolic potential, and amplicon length heterogeneity analysis, to estimate the molecular diversity of these communities. Both techniques demonstrated that the halophilic Bacteria and halophilic Archaea populations in the Eilat, Israel saltern are dynamic communities with extensive metabolic potentials and changing community structures. Halophilic Bacteria were detected in Mono Lake and the lower salinity ponds at the Shark Bay saltern in Western Australia, except when the crystallizer samples were stressed by exposure to Acid Green Dye #9899. At Shark Bay, halophilic Archaea were found only in the crystallizer samples. These data confirm both the metabolic diversity and the phylogenetic complexity of the microbial communities and assert the need to develop more versatile media for the cultivation of the diversity of bacteria in hypersaline environments. Journal of Industrial Microbiology & Biotechnology (2002) 28, 48–55 DOI: 10.1038/sj/jim/7000175 Received 20 May 2001/ Accepted in revised form 15 June 2001     

Effect of salinity on temporal and spatial dynamics of ammonia-oxidising bacteria from intertidal freshwater sediment

Temporal and spatial dynamics within an ammonia-oxidising community from intertidal, freshwater sediments were studied in microcosms simulating flooding twice a day with fresh, brackish and marine waters. The microcosms had been filled with the upper 5 cm of intertidal freshwater sediment from the river Scheldt. Changes in community composition were examined by denaturing gradient gel electrophoresis of amplified DNA from the community. In the first week of incubation the initially present members of the Nitrosomonas oligotropha lineage were replaced by other members of the same lineage in the top layer of the sediment subjected to flooding with freshwater. Prolonged incubation extended niche differentiation to a depth of 5 cm. In the microcosms flooded with saline media, the initially present members of the N. oligotropha lineage were replaced by strains belonging to the Nitrosomonas marina lineage, but only in the top 1cm. Shift in community composition occurred earlier in the marine microcosms than in the brackish microcosms and was slower than the change in the freshwater microcosms. Irrespective of the nature of the flooding medium, shifts in community composition were always consistent among replicate microcosms. We conclude that salinity is an important steering factor in niche differentiation among ammonia-oxidising bacteria and also that changes within the community of this functional group of bacteria may occur at different rates.     

Assembly processes and source tracking of planktonic and benthic bacterial communities in the Yellow River estuary

Estuaries connect rivers with the ocean and are considered transition regions due to the continuous inputs from rivers. Microbiota from different sources converge and undergo succession in these transition regions, but their assembly mechanisms along environmental gradients remain unclear. Here, we found that salinity had a stronger effect on planktonic than on benthic microbial communities, and the dominant planktonic bacteria changed more distinctly than the dominant benthic bacteria with changes in salinity. The planktonic bacteria in the brackish water came mainly from seawater, which was confirmed in the laboratory, whereas the benthic bacteria were weakly affected by salinity, which appeared to be a mixture of the bacteria from riverine and oceanic sediments. Benthic bacterial community assembly in the sediments was mainly controlled by homogeneous selection and almost unaffected by changes in salinity, the dominant assemblage processes for planktonic bacteria changed dramatically along the salinity gradient, from homogeneous selection in freshwater to drift in seawater. Our results highlight that salinity is the key driver of estuarine microbial succession and that salinity is more important in shaping planktonic than benthic bacterial communities in the Yellow River estuary.     

A comprehensive census of lake microbial diversity on a global scale

Despite recent interest in microbial diversity and community structure of lakes across various spatial scales, a global biogeographic distribution pattern and its controlling factors have not been fully disclosed. Here, we compiled and analyzed 88,334,735 environmental 16S rRNA sequences from 431 lakes across a wide range of geographical distance and environmental conditions(in particular, salinity, 0–373.3 gL~(–1)). Our results showed that lake sediments inhabit significantly(ANOVA: P0.001) more diverse microbial communities than lake waters. Non-metric dimensional scaling(NMDS) ordinations indicated that microbial community compositions differed distinctly among sample types(freshwater vs. saline, water vs. sediment) and geographic locations. Mantel and partial Mantel tests showed that microbial community composition in lake water was significantly(P=0.001) correlated with geographic distance, salinity, and pH. Statistical analyses based on neutral community and null models indicated that stochastic processes may play predominant roles in shaping the microbial biogeographic distribution patterns in the studied global lake waters. The dispersal-related stochasticity(e.g., homogenizing dispersal) exhibited a stronger influence on the distribution of microbial community in freshwater lakes than in saline lakes. Overall, this work expands our understanding of the impact of geographic distance, environmental conditions, and stochastic processes on microbial distribution in global lakes.     

The Gut Microbial Community of Midas Cichlid Fish in Repeatedly Evolved Limnetic-Benthic Species Pairs

Gut bacterial communities are now known to influence a range of fitness related aspects of organisms. But how different the microbial community is in closely related species, and if these differences can be interpreted as adaptive is still unclear. In this study we compared microbial communities in two sets of closely related sympatric crater lake cichlid fish species pairs that show similar adaptations along the limnetic-benthic axis. The gut microbial community composition differs in the species pair inhabiting the older of two crater lakes. One major difference, relative to other fish, is that in these cichlids that live in hypersaline crater lakes, the microbial community is largely made up of Oceanospirillales (52.28%) which are halotolerant or halophilic bacteria. This analysis opens up further avenues to identify candidate symbiotic or co-evolved bacteria playing a role in adaptation to similar diets and life-styles or even have a role in speciation. Future functional and phylosymbiotic analyses might help to address these issues.     

Diversity of sulfur-cycle prokaryotes in freshwater lake sediments investigated using aprA as the functional marker gene

The diversity of sulfate-reducing prokaryotes (SRPs) and sulfur-oxidizing prokaryotes (SOPs) in freshwater lake ecosystems was investigated by cloning and sequencing of the aprA gene, which encodes for a key enzyme in dissimilatory sulfate reduction and sulfur oxidation. To understand their diversity better, the spatial distribution of aprA genes was investigated in sediments collected from six geographically distant lakes in Antarctica and Japan, including a hypersaline lake for comparison. The microbial community compositions of freshwater sediments and a hypersaline sediment showed notable differences. The clones affiliated with Desulfobacteraceae and Desulfobulbaceae were frequently detected in all freshwater lake sediments. The SOP community was mainly composed of four major phylogenetic groups. One of them formed a monophyletic cluster with a sulfur-oxidizing betaproteobacterium, Sulfuricella denitrificans, but the others were not assigned to specific genera. In addition, the AprA sequences, which were not clearly affiliated to either SRP or SOP lineages, dominated the libraries from four freshwater lake sediments. The results showed the wide distribution of some sulfur-cycle prokaryotes across geographical distances and supported the idea that metabolic flexibility is an important feature for SRP survival in low-sulfate environments.