Archaeal diversity along a subterranean salt core from the Salar Grande (Chile)

The Salar Grande in the Coastal Range of Northern Chile is a fossil evaporitic basin filled with almost pure halite (95% NaCl average). It is assumed that the basin has not received input of brines since the Pliocene (5.3 to 1.8 million years). Below 1 m the halite has remained undissolved since this time, whereas the upper layer has been dissolved and recrystallized by dripping fogs and occasional rainfall. We compared the archaeal community at different depths using both nested PCR and cultivation. The upper 10 cm of halite crust contained diverse haloarchaeal species, including several from new genera, but their provenance is unknown. For samples deeper in the core, a new and rigorous procedure for chemically sterilizing the surface of single halite crystals was developed. These halite crystals contained only species of the genus Halobacterium (Hbt.). Halobacterium salinarum-like sequences were detected by PCR, and evidence that they were from ancient DNA include: comparison with numerous negative controls; detection of 16S rRNA sequence differences in non-conserved regions, indicating genuine evolutionary mutations rather than PCR-cloning artefacts; independent isolation of Hbt. salinarum from ancient halite; and diverse mechanisms possessed by this species for minimizing radiation damage and thus enhancing its potential for long-term survival. Haloarchaea related to Hbt. noricense were obtained from enrichment cultures from ≈ 0.4 and 15.4 m depth. We investigated Hbt. noricense strain A1 and found that when trapped inside halite crystals its recovery was as rapid after 27 months of entombment as at day 0, faring much better than other extreme halophiles. A biogeographical investigation showed that Hbt. noricense-like organisms were: commonly found in surface-sterilized ancient halite, associated with salt mines, in halite crusts, and, despite a much more intense search, only rarely detected in surface environments. We conclude that some Halobacterium species are specialists at long-term survival in halite.     

Changes in bacterial and archaeal communities during the concentration of brine at the graduation towers in Ciechocinek spa (Poland)

This study evaluates the changes in bacterial and archaeal community structure during the gradual evaporation of water from the brine (extracted from subsurface Jurassic deposits) in the system of graduation towers located in Ciechocinek spa, Poland. The communities were assessed with 16S rRNA gene sequencing (MiSeq, Illumina) and microscopic methods. The microbial cell density determined by direct cell count was at the order of magnitude of 10⁷ cells/mL. It was found that increasing salt concentration was positively correlated with both the cell counts, and species-level diversity of bacterial and archaeal communities. The archaeal community was mostly constituted by members of the phylum Euryarchaeota, class Halobacteria and was dominated by Halorubrum-related sequences. The bacterial community was more diverse, with representatives of the phyla Proteobacteria and Bacteroidetes as the most abundant. The proportion of Proteobacteria decreased with increasing salt concentration, while the proportion of Bacteroidetes increased significantly in the more concentrated samples. Representatives of the genera Idiomarina, Psychroflexus, Roseovarius, and Marinobacter appeared to be tolerant to changes of salinity. During the brine concentration, the relative abundances of Sphingobium and Sphingomonas were significantly decreased and the raised contributions of genera Fabibacter and Fodinibius were observed. The high proportion of novel (not identified at 97% similarity level) bacterial reads (up to 42%) in the 16S rRNA gene sequences indicated that potentially new bacterial taxa inhabit this unique environment.

     

Microbial diversity and activity in seafloor brine lake sediments (Alaminos Canyon block 601, Gulf of Mexico)

The microbial communities thriving in deep‐sea brines are sustained largely by energy rich substrates supplied through active seepage. Geochemical, microbial activity, and microbial community composition data from different habitats at a Gulf of Mexico brine lake in Alaminos Canyon revealed habitat‐linked variability in geochemistry that in turn drove patterns in microbial community composition and activity. The bottom of the brine lake was the most geochemically extreme (highest salinity and nutrient concentrations) habitat and its microbial community exhibited the highest diversity and richness indices. The habitat at the upper halocline of the lake hosted the highest rates of sulfate reduction and methane oxidation, and the largest inventories of dissolved inorganic carbon, particulate organic carbon, and hydrogen sulfide. Statistical analyses indicated a significant positive correlation between the bacterial and archaeal diversity in the bottom brine sample and inventories. Other environmental factors with positive correlation with microbial diversity indices were DOC, H₂S, and DIC concentrations. The geochemical regime of different sites within this deep seafloor extreme environment exerts a clear selective force on microbial communities and on patterns of microbial activity.     

Biogeography at the limits of life: Do extremophilic microbial communities show biogeographical regionalization?

Aim

Biogeographical regions are the fundamental geographical units for grouping Earth's biodiversity. Biogeographical regionalization has been demonstrated for many higher taxa, such as terrestrial plants and vertebrates, but not in microbial communities. Therefore, we sought to test empirically whether microbial communities, or taxa, show patterns consistent with biogeographical regionalization.

Location

Within halite (NaCl) crystals from coastal solar salterns of western Europe, the Mediterranean and east Africa.

Time period

Modern (2006–2013).

Major taxa studied

Archaea.

Methods

Using high‐throughput Illumina amplicon sequencing, we generated the most high‐resolution characterization of halite‐associated archaeal communities to date, using samples from 17 locations. We grouped communities into biogeographical clusters based on community turnover to test whether these communities show biogeographical regionalization. To examine whether individual taxa, rather than communities, show biogeographical patterns, we also tested whether the relative abundance of individual genera may be indicative of a community's biogeographical origins using machine learning methods, specifically random forest classification.

Results

We found that the rate of community turnover was greatest over subregional spatial scales (< 500 km), whereas at regional spatial scales the turnover was independent of geographical distance. Biogeographical clusters of communities were either not statistically robust or lacked spatial coherence, inconsistent with biogeographical regionalization. However, we identified several archaeal genera that were good indicators of biogeographical origin, providing classification error rates of < 10%.

Main conclusions

Overall, our results provide little support for the concept of biogeographical regions in these extremophilic microbial communities, despite the fact that some taxa do show biogeographical patterns. We suggest that variable dispersal ability among the halite‐associated Archaea may disrupt biogeographical patterns at the community level, preventing the formation of biogeographical regions. This means that the processes that lead to the formation of biogeographical regions operate differentially on individual microbial taxa rather than on entire communities.     

Archaeal diversity along a soil salinity gradient prone to disturbance

We employed a cultivation-independent approach to examine archaeal diversity along a transient soil salinity gradient at Salt Spring in British Columbia, Canada that is routinely eroded due to heavy, recurrent rainfall. Archaeal 16S rRNA gene libraries were created using DNA extracted from three soil samples collected along this gradient. Statistical comparisons indicated similar archaeal richness across sites but, a significant shift in archaeal community composition along the salinity gradient. Seven distinct phylogenetic groups were represented in soil libraries. Haloarchaea were the most commonly sampled group. Other 16S rRNA sequences were related to uncultured Euryarchaeota and Crenarchaeota or halophilic methanogens. Haloarchaeal diversity was remarkably high in soil of elevated salinity compared with previously characterized haloarchaeal communities. Salt Spring haloarchaea were not closely related to known low-salt adapted/tolerant species, suggesting they may be frequently faced with local mortality as a result of frequent declines in soil salinity. We speculate that ecosystem disturbance -- in the form of salinity fluctuations -- is one mechanism for maintaining a diverse community of haloarchaea at Salt Spring.     

Microbial diversity of an Antarctic subglacial community and high-resolution replicate sampling inform hydrological connectivity in a polar desert

Antarctic subglacial environments host microbial ecosystems and are proving to be geochemically and biologically diverse. The Taylor Glacier, Antarctica, periodically expels iron-rich brine through a conduit sourced from a deep subglacial aquifer, creating a dramatic red surface feature known as Blood Falls. We used Illumina MiSeq sequencing to describe the core microbiome of this subglacial brine and identified previously undetected but abundant groups including the candidate bacterial phylum Atribacteria and archaeal phylum Pacearchaeota. Our work represents the first microbial characterization of samples collected from within a glacier using a melt probe, and the only Antarctic subglacial aquatic environment that, to date, has been sampled twice. A comparative analysis showed the brine community to be stable at the operational taxonomic unit level of 99% identity over a decade. Higher resolution sequencing enabled deconvolution of the microbiome of subglacial brine from mixtures of materials collected at the glacier surface. Diversity patterns between this brine and samples from the surrounding landscape provide insight into the hydrological connectivity of subglacial fluids to the surface polar desert environment. Understanding subice brines collected on the surfaces of thick ice covers has implications for analyses of expelled materials that may be sampled on icy extraterrestrial worlds.     

Culturable bacteriorhodopsin-producing haloarchaea of Tuz Lake (Turkey)

Abstract

Lake Tuz, the largest hypersaline lake in Turkey, has a great variety of microbial communities that adapted to its extreme environment and produce many industrially important compounds such as photosensitive bacteriorhodopsins. So far, the information about the bacteriorhodopsin-producing haloarchaea species of the lake is still limited. In the present study, archaeal bacteriorhodopsin producers were isolated from three locations of the lake. Their bacteriorhodopsin-producing capability was validated by the purification and SDS-PAGE analysis of the delipidated bacteriorhodopsin molecule. The active isolates were identified by the sequencing of partial 16S rDNA gene regions. According to the results, 11 bacteriorhodopsin-producing isolates grouped in Halobacterium salinarum (4), Halobacterium sp. (3), Haloarcula salaria (2), Haloarcula sp. (1) and Halorubrum sp. (1). Our research demonstrated that Lake Tuz is an important natural source of bacteriorhodopsin-producing haloarchaea and the isolates can be valuable for the related technological applications.     

Cursorial spiders and succession: age or habitat structure?

Summary The structure of cursorial spider assemblages was examined along a gradient of four temperature successional communities. Species diversity (H), richness (S), and evenness (J) exhibited a dichotomy between herbaceous and woody communities rather than a progressive change with community age: all three parameters were higher in the two younger fields than in the two older woodlands, which is contrary to conventional successional theory. Species importance curves were steeper in the two woody communities. The breadth of the distribution of adult body lengths was greater in the two herbaceous communities. Indices of community similarity revealed neither a successional trend nor the vegetative dichotomy. We suggest the hypothesis that habitat structure is a more important determinant of cursorial spider diversity than successional age per se, and that the switch in dominance from herbaceous to woody vegetation is the critical change. We further suggest that competition for prey is more important to cursorial spiders in early successional (herbaceous) communities, because of a switch in the limiting resource from prey in these communities to the amount of accumulating litter (a spatial resource) in older woody stands. This may explain the greater variation in adult body size of these generalist predators in the two younger communities.     

Effects of UV radiation on the structure of Arctic macrobenthic communities

At present, information on the effects of ultraviolet radiation (UVR) on structure and diversity of polar, in particular Arctic, benthic communities is scarce. It is unclear whether and to what extent communities of different successional age are susceptible to UVR and whether UVR effects known to be detrimental at the species level can be buffered at the community level. In a subtidal field study on Spitsbergen (Norwegian Arctic), we investigated the potential effect of distinct UVR regimes on macrobenthic communities of different successional ages, grown on ceramic tiles. Total taxon cover, taxon composition, evenness, and richness were assessed after experimental exposure of 4 and 8 weeks. Overall, 17 algal and invertebrate taxa were encountered in the study and diatoms dominated the communities regardless of successional age or radiation treatment. UVR effects were dependent on both exposure time and community age. We did not find overall detrimental UVB effects. In contrast, abundance of several species increased in UVR-exposed communities. Especially, UVA seemed to have a beneficial effect in that several green and brown algal taxa increased in abundance (e.g. Ulothrix flacca, Chlorophyta, and Desmarestia sp., Phaeophyceae). In general, UVR effects depended on species composition and thus on successional age of communities, with later successional communities likely to be able to buffer and alleviate possible negative effects of UVR at species level. Overall, the presented study provides a first insight into the complex role UVR plays in structuring Arctic epibenthic communities.     

Biodiversity in different successional stages of Mediterranean enclaves distributed along Sinop Peninsula (Turkey)

The aim of this research was to evaluate plant diversity and the relationships between the distribution of Raunkiaer life forms and community structure, and species richness, at different successional stages in communities of Quercus ilex L., Erica arborea L. and Sarcopoterium spinosum (L.) Spach., distributed as enclaves in Sinop Province. Permanent sample plots were selected to determine plant diversity. The cover percentage of each plant species was recorded monthly during two vegetation periods. Raunkiaer life forms, and the Shannon–Wiener, Evenness, Simpson and Margalef indexes were determined. Twenty-three species in Quercus ilex, 96 species in Erica arborea, and 148 species in Sarcopoterium spinosum were identified. Hemicryptophyte dominancy was observed followed by phanerophytes in the Q. ilex community, and therophyte and hemicryptophyte dominancy in the E. arborea and S. spinosum communities, respectively. It was determined that the S. spinosum community was the most heterogeneous community while the Q. ilex community was more uniform than other communities. The variation in diversity indexes, homogeneity, and composition of life forms among communities adopting a similar climatic environment could result from a differentiation of environmental factors, which impact on community structuring, from biotic to abiotic at different successional stages of Mediterranean communities.     

The effects of some soil properties (soil nitrogen forms and moisture) on community structure in Mediterranean plant communities in the Black Sea region

Mediterranean ecosystems comprise the second biodiversity hotspot area after tropical rain forests and will be most affected by global climate change. Therefore, it is important to understand community dynamics for effective conservation in this region. We investigated the relationships between soil moisture, nitrogen forms and community structuring in Quercus ilexL., Erica arborea L. and Sarcopoterium spinosum (L.) Spach communities, representing different successional stages, distributed as Mediterranean enclaves on the Sinop Peninsula (Turkey). The soil moisture, ammonium, nitrate and nitrite content were measured seasonally. Differences in these abiotic parameters within and between communities over seasons were tested. Previously collected biotic data were then used to analyze the relationship between soil parameters and community structure. Significant differences in soil parameters within and between seasons were found within and between communities. Our results show that there are different relationships between soil moisture, nitrogen forms and community structure in Mediterranean plant communities representing different successional stages. Differentiation in vegetation structure during succession cause changes especially in the water and nitrate content of the soil, and these changes in turn affect the continuity of community structure in Mediterranean plant communities.     

Microbial diversity in degraded and non-degraded petroleum samples and comparison across oil reservoirs at local and global scales

Microorganisms have shown their ability to colonize extreme environments including deep subsurface petroleum reservoirs. Physicochemical parameters may vary greatly among petroleum reservoirs worldwide and so do the microbial communities inhabiting these different environments. The present work aimed at the characterization of the microbiota in biodegraded and non-degraded petroleum samples from three Brazilian reservoirs and the comparison of microbial community diversity across oil reservoirs at local and global scales using 16S rRNA clone libraries. The analysis of 620 16S rRNA bacterial and archaeal sequences obtained from Brazilian oil samples revealed 42 bacterial OTUs and 21 archaeal OTUs. The bacterial community from the degraded oil was more diverse than the non-degraded samples. Non-degraded oil samples were overwhelmingly dominated by gammaproteobacterial sequences with a predominance of the genera Marinobacter and Marinobacterium. Comparisons of microbial diversity among oil reservoirs worldwide suggested an apparent correlation of prokaryotic communities with reservoir temperature and depth and no influence of geographic distance among reservoirs. The detailed analysis of the phylogenetic diversity across reservoirs allowed us to define a core microbiome encompassing three bacterial classes (Gammaproteobacteria, Clostridia, and Bacteroidia) and one archaeal class (Methanomicrobia) ubiquitous in petroleum reservoirs and presumably owning the abilities to sustain life in these environments.

     

荒漠孑遗植物四合木对土壤古菌群落的影响

土壤是植物定居的场所,也是植物-微生物互作的重要界面。古菌是土壤微生物重要组份,在碳、氮、硫、铁等元素的生物地球化学循环和植物的生长发育、适应生境中发挥重要作用。植物定居对土壤古菌群落的影响研究鲜有开展,孑遗植物在研究植物-微生物-环境互作中具有独特的优势。采用扩增子高通量测序技术,研究以荒漠孑遗植物四合木为建群种或优势种的四合木-红砂-珍珠-针茅群落、四合木-针茅群落和四合木群落等三种荒漠植物群落类型中,四合木根区土壤和光板地土体土壤古菌群落特征,揭示四合木定居对土壤古菌物种数量、多样性、群落组成及功能的影响。结果表明,荒漠孑遗植物四合木定居不仅增加了根区土壤古菌的物种数量,提高了根区土壤古菌群落多样性,而且改变了土壤古菌群落组成,减少了奇古菌门Nitrososphaeraceae科未分类的属氨氧化古菌（unclassified_f_Nitrososphaeraceae）和暂定Nitrososphaera属氨氧化古菌（Candidatus Nitrososphaera）相对丰度,增加了Nitrososphaeraceae科暂定Nitrocosmicus属氨氧化古菌（Candidatus Nitrocosmicus）和广古菌门海洋古菌类群Ⅱ中未分类的属（norank_o_Marine_Group_II）相对丰度,广古菌门热原体纲未分类的属（unclassified_c__Thermoplasmata）相对丰度变化显著。植物群落演替对四合木根区土壤和光板地土体土壤古菌群落均无显著影响。Nitrososphaeraceae科氨氧化古菌是三种不同荒漠植物群落类型中土壤古菌的核心微生物组。四合木定居也显著改变土壤古菌群落的功能,减弱了高丰度功能,增强了低丰度功能,对有氧呼吸、核苷酸合成、氨基酸合成等途径影响显著。荒漠孑遗植物四合木定居改变了土壤古菌群落物种数量、多样性、组成、功能等特征。     

Primary succession of Bistorta vivipara (L.) Delabre (Polygonaceae) root‐associated fungi mirrors plant succession in two glacial chronosequences

Glacier chronosequences are important sites for primary succession studies and have yielded well‐defined primary succession models for plants that identify environmental resistance as an important determinant of the successional trajectory. Whether plant‐associated fungal communities follow those same successional trajectories and also respond to environmental resistance is an open question. In this study, 454 amplicon pyrosequencing was used to compare the root‐associated fungal communities of the ectomycorrhizal (ECM) herb Bistorta vivipara along two primary succession gradients with different environmental resistance (alpine versus arctic) and different successional trajectories in the vascular plant communities (directional replacement versus directional non‐replacement). At both sites, the root‐associated fungal communities were dominated by ECM basidiomycetes and community composition shifted with increasing time since deglaciation. However, the fungal community's successional trajectory mirrored the pattern observed in the surrounding plant community at both sites: the alpine site displayed a directional‐replacement successional trajectory, and the arctic site displayed a directional‐non‐replacement successional trajectory. This suggests that, like in plant communities, environmental resistance is key in determining succession patterns in root‐associated fungi. The need for further replicated study, including in other host species, is emphasized.     

Exotic plants establish persistent communities

Many exotic plants utilize early successional traits to invade disturbed sites, but in some cases these same species appear able to prevent re-establishment of late-successional and native species. Between 2002 and 2004, I studied 25 fields that represent a 52-year chronosequence of agricultural abandonment in a shrub-steppe ecosystem in Washington State, USA, to determine if exotic plants behaved as early successional species (i.e., became less abundant over time) or if they established persistent communities. Exotics maintained dominance in tilled (73% of total cover) relative to never-tilled (6% of total cover) fields throughout the chronosequence. Exotic community composition, however, changed on annual and decadal timescales. Changes in exotic community composition did not reflect typical successional patterns. For example, some exotic perennial species (e.g., Centaurea diffusa and Medicago sativa) were less common and some exotic annual species (e.g., Sissymbrium loeselii and S. altissimum) were more common in older relative to younger fields. Exotics in the study area appeared to establish communities that are resistant to re-invasion by natives, resilient to losses of individual exotic species, and as a result, maintain total exotic cover over both the short- and long-term: exotics replaced exotics. Exotics did not invade native communities and natives did not invade exotic communities across the chronosequence. These results suggest that, in disturbed sites, exotic plants establish an alternative community type that while widely variable in composition, maintains total cover over annual and decadal timescales. Identifying alternative state exotic communities and the mechanisms that explain their growth is likely to be essential for native plant restoration.     

Bacterial Succession on the Leaf Surface: A Novel System for Studying Successional Dynamics

Succession is a widely studied process in plant and animal systems, but succession in microbial communities has received relatively little attention despite the ubiquity of microorganisms in natural habitats. One important microbial habitat is the phyllosphere, or leaf surface, which harbors large, diverse populations of bacteria and offers unique opportunities for the study of succession and temporal community assembly patterns. To explore bacterial community successional patterns, we sampled phyllosphere communities on cottonwood (Populus deltoides) trees multiple times across the growing season, from leaf emergence to leaf fall. Bacterial community composition was highly variable throughout the growing season; leaves sampled as little as a week apart were found to harbor significantly different communities, and the temporal variability on a given tree exceeded the variability in community composition between individual trees sampled on a given day. The bacterial communities clearly clustered into early-, mid-, and late-season clusters, with early- and late-season communities being more similar to each other than to the mid-season communities, and these patterns appeared consistent from year to year. Although we observed clear and predictable changes in bacterial community composition during the course of the growing season, changes in phyllosphere bacterial diversity were less predictable. We examined the species–time relationship, a measure of species turnover rate, and found that the relationship was fundamentally similar to that observed in plant and invertebrate communities, just on a shorter time scale. The temporal dynamics we observed suggest that although phyllosphere bacterial communities have high levels of phylogenetic diversity and rapid turnover rates, these communities follow predictable successional patterns from season to season.     

Spatial Distribution and Molecular Diversity of Archaeal Communities in the Extreme Hypersaline Meromictic Brâncoveanu Lake (Transylvanian Basin,Romania)

Dating from the Middle Miocene, the massive halite deposits lying beneath the Transylvanian Basin (Central Romania) have been valuable mineral resources quarried for millennia. Among the numerous hypersaline pit lakes that resulted from this mining, Brâncoveanu Lake is unique by its extreme salinity. Assessment of physicochemical variables, water chemistry and trophic status indicated that Brâncoveanu Lake is a permanently stratified, pH-neutral, NaCl-rich and eutrophied system. We investigated the abundance, molecular diversity and vertical distribution of archaeal community by culture-independent approaches. Additionally, the most relevant environmental parameters shaping the archaeal community composition were evaluated by statistical methods. Archaea appeared to largely outnumber Bacteria; altogether the great prevalence of Halobacteriaceae-related sequences could imply a major contribution of this group to the biogeochemical carbon turnover. The fairly distinct composition of archaeal communities reflects the lake's physicochemical stratification. Among the limnological factors, salinity and oxygen showed a significant impact on determining the composition and structure of archaeal assemblages. Furthermore, Brâncoveanu Lake might harbor novel microorganisms such as members of the recently described phylum Nanohaloarchaea. Overall, this study reported the occurrence of halophilic Archaea in a little explored hydrogeochemical system and provided a better insight into geomicrobiology of meromictic hypersaline pit lakes.     

Spatiotemporal variation of bacterial and archaeal communities in sediments of a drinking reservoir,Beijing, China

Bacterial and archaeal assemblages are one of the most important contributors to the recycling of nutrients and the decomposition of organic matter in aquatic sediments. However, their spatiotemporal variation and its driving factors remain unclear, especially for drinking reservoirs, which are strongly affected by human consumption. Using quantitative PCR and Illumina MiSeq sequencing, we investigated the bacterial and archaeal communities in the sediments of a drinking reservoir, the Miyun Reservoir, one of the most important drinking sources for Beijing City. The abundance of bacteria and archaea presented no spatiotemporal variation. With respect to community diversity, visible spatial and temporal differences were observed in archaea, whereas the bacterial community showed minor variation. The bacterial communities in the reservoir sediment mainly included Proteobacteria, Bacteroidetes, Nitrospirae, Acidobacteria, and Verrucomicrobia. The bacterial community structure showed obvious spatial variation. The composition of the bacterial operational taxonomic units (OTUs) and main phyla were dam-specific; the composition of samples in front of the dam were significantly different from the composition of the other samples. The archaeal communities were mainly represented by Woesearchaeota and Euryarchaeota. Distinctly spatial and seasonal variation was observed in the archaeal community structure. The sediment NH₄ ⁺–N, pH, and water depth were identified as the key driving factors of changes in the composition of the bacterial and archaeal communities. Water depth might have the greatest influence on the microbial community structure. The dam-specific community structure may be related to the greater water depth in front of the dam. This finding indicates that water depth might be the greatest contributor to the microbial community structure in the Miyun Reservoir.