Prokaryotic Diversity Research Articles

Response of Hypolimnetic Water and Bottom Sediment Microbial Communities to Freshwater Salinization—A Microcosm Experiment

The introduction of NaCl in freshwater caused by winter runoffs is a problem whose consequences are still little understood. We sought to analyze the effect of NaCl addition on microbial communities of the hypolimnion and bottom sediments of a Canadian lake. Using microcosms comprising a salinity gradient varying between 0.01 and 3.22 ppt (10–3220 mg/L−1) NaCl, we investigated the effect of salinity on prokaryotic absolute abundance and diversity, following a three- and six-week exposure, and detected the presence of a salinity threshold for microbial communities’ differentiation. We observed a significant decline of bacterial diversity after six weeks in hypolimnetic samples. In the sediments, no clear effect of NaCl was observed on abundance or diversity, despite the presence of variations throughout the salinity gradient. The implication of nutrient fluctuations as well as the co-occurrence of species and inter-domain interactions is likely and would strongly contribute to the development of salt-exposed prokaryotic communities. In hypolimnetic water and sediments, the archaeal and eukaryotic communities differed significantly from 0.93 ppt (930 mg/L−1), while only conclusive at 1.9 ppt (1900 mg/L−1) NaCl in bacteria, meaning that the regulations in place are possibly suitable for the protection of the microbial communities in the hypolimnion and sediment lake layers.

From friends to foes: fungi could be emerging marine sponge pathogens under global change scenarios.

Global change, experienced in the form of ocean warming and pollution by man-made goods and xenobiotics, is rapidly affecting reef ecosystems and could have devastating consequences for marine ecology. Due to their critical role in regulating marine food webs and trophic connections, sponges are an essential model for studying and forecasting the impact of global change on reef ecosystems. Microbes are regarded as major contributors to the health and survival of sponges in marine environments. While most culture-independent studies on sponge microbiome composition to date have focused on prokaryotic diversity, the importance of fungi in holobiont behavior has been largely overlooked. Studies focusing on the biology of sponge fungi are uncommon. Thus, our current understanding is quite limited regarding the interactions and “crosstalk” between sponges and their associated fungi. Anthropogenic activities and climate change may reveal sponge-associated fungi as novel emerging pathogens. Global change scenarios could trigger the expression of fungal virulence genes and unearth new opportunistic pathogens, posing a risk to the health of sponges and severely damaging reef ecosystems. Although ambitious, this hypothesis has not yet been proven. Here we also postulate as a pioneering hypothesis that manipulating sponge-associated fungal communities may be a new strategy to cope with the threats posed to sponge health by pathogens and pollutants. Additionally, we anticipate that sponge-derived fungi might be used as novel sponge health promoters and beneficial members of the resident sponge microbiome in order to increase the sponge's resistance to opportunistic fungal infections under a scenario of global change.

Effects of biochar on soil microbial communities: A meta-analysis

Changes in soil microbial communities may impact soil fertility and stability because microbial communities are key to soil functioning by supporting soil ecological quality and agricultural production. The effects of soil amendment with biochar on soil microbial communities are widely documented but studies highlighted a high degree of variability in their responses following biochar application. The multiple conditions under which they were conducted (experimental designs, application rates, soil types, biochar properties) make it difficult to identify general trends. This supports the need to better determine the conditions of biochar production and application that promote soil microbial communities. In this context, we performed the first ever meta-analysis of the biochar effects on soil microbial biomass and diversity (prokaryotes and fungi) based on high-throughput sequencing data. The majority of the 181 selected publications were conducted in China and evaluated the short-term impact (<3 months) of biochar. We demonstrated that a large panel of variables corresponding to biochar properties, soil characteristics, farming practices or experimental conditions, can affect the effects of biochar on soil microbial characteristics. Using a variance partitioning approach, we showed that responses of soil microbial biomass and prokaryotic diversity were highly dependent on biochar properties. They were influenced by pyrolysis temperature, biochar pH, application rate and feedstock type, as wood-derived biochars have particular physico-chemical properties (high C:N ratio, low nutrient content, large pores size) compared to non-wood-derived biochars. Fungal community data was more heterogenous and scarcer than prokaryote data (30 publications). Fungal diversity indices were rather dependent on soil properties: they were higher in medium-textured soils, with low pH but high soil organic carbon. Altogether, this meta-analysis illustrates the need for long-term field studies in European agricultural context for documenting responses of soil microbial communities to biochar application under diverse conditions combining biochar types, soil properties and conditions of use.

Soil depths and developmental stages of biological soil crusts are more important than shrub cover in structuring prokaryotic communities

The influence of microhabitat factors on prokaryotic communities within desert ecosystems, particularly those residing in biological soil crusts (biocrusts), remains poorly understood. This study aimed to elucidate the relative importance of different microhabitats, including soil depths, biocrust developmental stages, and shrub cover, in shaping soil prokaryotic communities. To achieve this, we conducted an in-depth investigation of soil prokaryotic communities using high-throughput amplicon sequencing in the Tengger desert, China. Our results showed that difference of soil properties, prokaryotic alpha, beta diversities and abundances of taxa and functional groups primarily differed between soil depths and among biocrust developmental stages. Furthermore, the impact of shrub cover on the aforementioned parameters was found to be modified by biocrust development. Specifically, we observed higher soil nutrient levels in the upper biocrust layer compared to the subsoil, with a consistent increasing trend during biocrust development in both soil layers. Conversely, soil pH displayed contrasting patterns. Prokaryotic alpha diversity exhibited a V-shaped pattern with biocrust development, initially decreasing and then increasing, and was higher in the subsoil compared to the biocrust layer. Additionally, although prokaryotic alpha diversity showed differences between shrub cover or not, the specific effect depended on biocrust stages. Cyanobacteria, phototrophic and nitrogen-fixing prokaryotes were more abundant in the upper biocrust layer, following a unimodal pattern with biocrust development, initially increasing, and then decreasing; while Actinobacteriota and Acidobacteriota showed higher abundance in the subsoil, with varying trends between the two soil depths during biocrust development. Soil pH and total P emerged as key regulators of prokaryotic communities across different microhabitats. This study contributes to our comprehensive understanding of the complex dynamics governing prokaryotic communities in desert ecosystems.

Hard rock dark biosphere and habitability

The discovery that most of the prokaryotic diversity and biomass on Earth resides in the deep subsurface, calls for an improved definition of habitability, which should consider the existence of dark biospheres in other planets and moons of the Solar System and beyond. The discovery of “interior liquid water worlds” on some ice moons with waterless surfaces has piqued wide astrobiological interest, but the sporadic mentions of the possibility of life in the deep subsurface of rocky planets in recent habitability reviews calls for a methodical effort to develop sufficient knowledge, both scientific and technological, to include the dark biospheres in our habitability assessments. In this review we analyze recent developments and the methodologies employed to characterize Earth’s continental hard rock deep subsurface to both prepare the future exploration of the putative dark biosphere of Mars and to highlight its importance when evaluating planetary habitability.

Effects of herbicide butachlor application on the growth of periphytic biofilms and nitrogen loss in paddy systems

The application of butachlor as an herbicide in paddy fields is widely practiced, aiming to increase rice yield by directly or indirectly influencing the paddy environment. Periphytic biofilms, which form at the soil-water interface in paddy fields, are complex bioaggregates that play an important role in nitrogen (N) cycling. The objective of this study was to investigate the effect of butachlor on periphytic biofilm growth and N cycling under both light and dark conditions in the laboratory. The results revealed that butachlor application hindered the growth of periphytic biofilms and led to the dominance of Cyanobacteria as the primary prokaryotes, while inhibiting the development of eukaryotic Trebouxiophyceae. Furthermore, the application of butachlor reduced the richness and diversity of prokaryotes, but increased those of eukaryotes in periphytic biofilms. The light treatments exhibited higher total N loss because light favored periphytic biofilm growth and enhanced ammonium (NH4+) assimilation and nitrification. Additionally, butachlor application resulted in the increased retention of NH4+-N and nitrate (NO3-)-N and an increase in N loss via denitrification. The abundances of functional genes encoding enzymes such as ammonia monooxygenase, nitrite reductase, and nitrous oxide reductase were increased by butachlor application, favoring nitrification and denitrification processes. Overall, the results suggest that butachlor application leads to an increase in total N loss mainly through denitrification in paddy systems, particularly in the presence of periphytic biofilms. Thus, the results may provide valuable insights into the changes in periphytic biofilm growth and N cycling induced by butachlor, and future studies can further explore the potential implications of these changes in paddy soils.

Potential benefits and risks of solar photovoltaic power plants on arid and semi-arid ecosystems: an assessment of soil microbial and plant communities.

Exponential increase in photovoltaic installations arouses concerns regarding the impacts of large-scale solar power plants on dryland ecosystems. While the effects of photovoltaic panels on soil moisture content and plant biomass in arid ecosystems have been recognized, little is known about their influence on soil microbial communities. Here, we employed a combination of quantitative PCR, high-throughput sequencing, and soil property analysis to investigate the responses of soil microbial communities to solar panel installation. We also report on the responses of plant communities within the same solar farm. Our findings showed that soil microbial communities responded differently to the shading and precipitation-alternation effects of the photovoltaic panels in an arid ecosystem. By redirecting rainwater to the lower side, photovoltaic panels stimulated vegetation biomass and soil total organic carbon content in the middle and in front of the panels, positively contributing to carbon storage. The shade provided by the panels promoted the co-occurrence of soil microbes but inhibited the abundance of 16S rRNA gene in the soil. Increase in precipitation reduced 18S rRNA gene abundance, whereas decrease in precipitation led to decline in plant aboveground biomass, soil prokaryotic community alpha diversity, and dehydrogenase activity under the panels. These findings highlight the crucial role of precipitation in maintaining plant and soil microbial diversities in dryland ecosystems and are essential for estimating the potential risks of large-scale solar power plants on local and global climate change in the long term.

Microbial diversity in Antarctic Dry Valley soils across an altitudinal gradient.

The Antarctic McMurdo Dry Valleys are geologically diverse, encompassing a wide variety of soil habitats. These environments are largely dominated by microorganisms, which drive the ecosystem services of the region. While altitude is a well-established driver of eukaryotic biodiversity in these Antarctic ice-free areas (and many non-Antarctic environments), little is known of the relationship between altitude and microbial community structure and functionality in continental Antarctica. We analysed prokaryotic and lower eukaryotic diversity from soil samples across a 684 m altitudinal transect in the lower Taylor Valley, Antarctica and performed a phylogenic characterization of soil microbial communities using short-read sequencing of the 16S rRNA and ITS marker gene amplicons. Phylogenetic analysis showed clear altitudinal trends in soil microbial composition and structure. Cyanobacteria were more prevalent in higher altitude samples, while the highly stress resistant Chloroflexota and Deinococcota were more prevalent in lower altitude samples. We also detected a shift from Basidiomycota to Chytridiomycota with increasing altitude. Several genera associated with trace gas chemotrophy, including Rubrobacter and Ornithinicoccus, were widely distributed across the entire transect, suggesting that trace-gas chemotrophy may be an important trophic strategy for microbial survival in oligotrophic environments. The ratio of trace-gas chemotrophs to photoautotrophs was significantly higher in lower altitude samples. Co-occurrence network analysis of prokaryotic communities showed some significant differences in connectivity within the communities from different altitudinal zones, with cyanobacterial and trace-gas chemotrophy-associated taxa being identified as potential keystone taxa for soil communities at higher altitudes. By contrast, the prokaryotic network at low altitudes was dominated by heterotrophic keystone taxa, thus suggesting a clear trophic distinction between soil prokaryotic communities at different altitudes. Based on these results, we conclude that altitude is an important driver of microbial ecology in Antarctic ice-free soil habitats.

Study of the structural and functional diversity of microbial communities in Uruguayan soils with respect to phosphorus phytoavailability: Doctoral thesis abstract

Phosphorus (P) is essential for plant growth; its excessive use as a fertilizer in agricultural intensification has negatively impacted the environment and the economy. Soil microorganisms play a key role in P cycling, mediating its phytoavailability through enzymatic mechanisms. In this thesis, we studied: a) the structural diversity of prokaryotic communities in five soil units with different parent materials and nutritional status; b) the functional profiles of these communities linked to P cycling and their relationship with soil physicochemical properties; c) the distribution and abundance of eight key enzymes of P cycling in grasslands of Uruguay and the world. Prokaryotic communities were studied using a metagenomic approach (16S rRNA gene and total metagenome). The main results were: a) Soil structure, nutrient content, and water retention capacity influence the composition of prokaryotic communities, composed mainly of Archaea, Firmicutes, Acidobacteria, Actinobacteria and Verrucomicrobia, with variations in their abundance according to soil type. b) Functional profiles of the communities were modeled by the same physicochemical properties as taxonomic diversity; functional diversity was lower than taxonomic diversity, suggesting functional redundancy. c) PhoD alkaline phosphatase was the most abundant and phylogenetically widely distributed enzyme, followed by Nsap-A and Nsap-C acid phosphatases. A strong association was found between the abundance and diversity of genes encoding these three enzymes and pH, maximum temperature and evapotranspiration. The results indicate that structural and functional prokaryotic diversity is influenced by soil physicochemical properties and environmental variables, making its understanding essential for the sustainable management of the P cycle in agroecosystems of the Campos biome.

Microbial taxa related to natural hydrogen and methane emissions in serpentinite-hosted hyperalkaline springs of New Caledonia.

The southeastern part of New Caledonia main island (Grande Terre) is the location of a large ophiolitic formation that hosts several hyperalkaline springs discharging high pH (∼11) and warm (<40°C) fluids enriched in methane (CH4) and hydrogen (H2). These waters are produced by the serpentinization of the ultrabasic rock formations. Molecular surveys had previously revealed the prokaryotic diversity of some of these New Caledonian springs, especially from the submarine chimneys of Prony Bay hydrothermal field. Here we investigate the microbial community of hyperalkaline waters from on-land springs and their relationships with elevated concentrations of dissolved H2 (21.1-721.3 μmol/L) and CH4 (153.0-376.6 μmol/L). 16S rRNA gene analyses (metabarcoding and qPCR) provided evidence of abundant and diverse prokaryotic communities inhabiting hyperalkaline fluids at all the collected springs. The abundance of prokaryotes was positively correlated to the H2/CH4 ratio. Prokaryotes consisted mainly of bacteria that use H2 as an energy source, such as microaerophilic Hydrogenophaga/Serpentinimonas (detected in all sources on land) or anaerobic sulfate-reducing Desulfonatronum, which were exclusively found in the most reducing (Eh ref H2 ∼ -700 mV) and the most H2-enriched waters discharging at the intertidal spring of the Bain des Japonais. The relative abundance of a specific group of uncultured Methanosarcinales that thrive in serpentinization-driven ecosystems emitting H2, considered potential H2-consuming methanogens, was positively correlated with CH4 concentrations, and negatively correlated to the relative abundance of methylotrophic Gammaproteobacteria. Firmicutes were also numerous in hyperalkaline waters, and their relative abundance (e.g., Gracilibacter or Dethiobacter) was proportional to the dissolved H2 concentrations, but their role in the H2 budget remains to be assessed. The prokaryotic communities thriving in New Caledonia hyperalkaline waters are similar to those found in other serpentinite-hosted high-pH waters worldwide, such as Lost City (North Atlantic) and The Cedars (California).

Biodiesel Co‐Product (BCP) amendment drives beneficial soil microbiome assembly promoting acid soil health

AbstractBiodiesel Co‐Product (BCP) amendment has been shown to decrease both nitrate leaching and nitrous oxide (N2O) emissions in acidic soil; however, the effects of BCP on the soil microbiome have not been investigated thoroughly. In this study, we investigated the response of prokaryotic and fungal communities in aspects of structure, diversity, and co‐occurrence network to the BCP amendment following complete mixing application (0–18‐cm depth) of 1.5 mg BCP‐C g−1 and surface application (0–6‐cm depth) of 4.5 mg BCP‐C g−1 via high‐throughput 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. The amendment altered microbial communities significantly by increasing the relative abundances of Proteobacteria (Burkholderia) and Ascomycota (Trichoderma) in prokaryotic and fungal communities, respectively. Only a higher rate application (4.5 mg BCP‐C g−1) decreased prokaryotic alpha diversity, whereas all rates of amendment decreased fungal diversity. The co‐occurrence network of prokaryotes had more nodes and links and a higher average degree and clustering coefficient than the fungal network with BCP addition. The majority of keystone species in prokaryotic and fungal networks were from Proteobacteria and Ascomycota taxa. Of note, the BCP amendment significantly increased the OTU numbers of potential biocontrol agents, including Trichoderma (T.) spirale, T. koningiopsis, and T. virens, etc., while decreased OTU numbers related to plant pathogens species, particularly in the complete mixing application. Our work highlights the potential for BCP amendments to promote the assembly of a healthy soil microbiome by enhancing the abundance of potential biocontrol microbes while reducing plant pathogens species, which may contribute to soil health.

Global analysis of the biosynthetic chemical space of marine prokaryotes

BackgroundMarine prokaryotes are a rich source of novel bioactive secondary metabolites for drug discovery. Recent genome mining studies have revealed their great potential to bio-synthesize novel secondary metabolites. However, the exact biosynthetic chemical space encoded by the marine prokaryotes has yet to be systematically evaluated.ResultsWe first investigated the secondary metabolic potential of marine prokaryotes by analyzing the diversity and novelty of the biosynthetic gene clusters (BGCs) in 7541 prokaryotic genomes from cultivated and single cells, along with 26,363 newly assembled medium-to-high-quality genomes from marine environmental samples. To quantitatively evaluate the unexplored biosynthetic chemical space of marine prokaryotes, the clustering thresholds for constructing the biosynthetic gene cluster and molecular networks were optimized to reach a similar level of the chemical similarity between the gene cluster family (GCF)-encoded metabolites and molecular family (MF) scaffolds using the MIBiG database. The global genome mining analysis demonstrated that the predicted 70,011 BGCs were organized into 24,536 mostly new (99.5%) GCFs, while the reported marine prokaryotic natural products were only classified into 778 MFs at the optimized clustering thresholds. The number of MF scaffolds is only 3.2% of the number of GCF-encoded scaffolds, suggesting that at least 96.8% of the secondary metabolic potential in marine prokaryotes is untapped. The unexplored biosynthetic chemical space of marine prokaryotes was illustrated by the 88 potential novel antimicrobial peptides encoded by ribosomally synthesized and post-translationally modified peptide BGCs. Furthermore, a sea-water-derived Aquimarina strain was selected to illustrate the diverse biosynthetic chemical space through untargeted metabolomics and genomics approaches, which identified the potential biosynthetic pathways of a group of novel polyketides and two known compounds (didemnilactone B and macrolactin A 15-ketone).ConclusionsThe present bioinformatics and cheminformatics analyses highlight the promising potential to explore the biosynthetic chemical diversity of marine prokaryotes and provide valuable knowledge for the targeted discovery and biosynthesis of novel marine prokaryotic natural products.8qkWfGqcrPbn_o7-XLBWPjVideo

Impact of elevated atmospheric CO2 on the wheat rhizomicrobiome under the additional influence of warming, drought, and nitrogen fertilization

The rhizomicrobiome is an important component of agricultural soil that may face vulnerability due to global change. Here, we focused on its response in a 2-year cropland free air carbon dioxide enrichment (FACE) experiment on winter wheat in combination with warming (+3 °C) and drought. To characterize bacterial abundance and prokaryotic diversity, 16S rRNA gene PCR amplicons obtained from soil DNA were analysed. Elevated CO2 (e[CO2]) increased under conventional water supply bacterial abundance, along with higher above-ground plant biomass, but had no tangible effect on the overall diversity and community composition. In contrast, drought reduced bacterial abundance under e[CO2] despite higher plant biomass, while it did not affect bacterial abundance at ambient CO2. Warming and N-fertilizer supplies increased bacterial abundance and community composition, but these responses were not modified by CO2. Compared to the wheat growth stage and variation in N-supply, the effect of CO2 on the overall community composition was minor, explaining 2.2% of its variation. While 7 taxa, representing only 0.3% of relative abundance and most of them affiliated with Acidobacteria, changed with the CO2 level, many more responded to growth stages and nitrogen supply. Fewer growth stage and N supply-responsive taxa were detected with e[CO2]. Our results provide strong evidence that wheat plant responses to e[CO2] transfer to the rhizomicrobiome affecting the abundance composition of their constituting microbes. Additional drought conditions can strongly change the direction of these responses and should thus be considered for predicting implications of global change for the cropland soil microbiomes.

Prokaryotic and Eukaryotic Communities Characteristic in the Water Column and Sediment along the Xiangjiang River, China

Microbial communities are central components of river ecosystems. They are involved in the transportation and transformation of certain pollutants, including nutrients discharged into surface water. Knowledge of microbial community structures is vital for understanding biochemical circulation in aquatic ecosystems. However, most of the research that is currently being conducted focuses more on bacterial diversity and less on eukaryotes, which also play key roles in the nutrient cycle. In this study, 10 sampling sites along the Xiangjiang River were selected, covering the entire reaches of Changsha City, China. Both prokaryotic and eukaryotic diversity and composition in the water and sediment samples were investigated. The results showed that conductivity, TN, and NH4+-N were the main environmental parameters influencing the distribution of microbial communities in the river water column. Proteobacteria, Acidobacteria, and Actinobacteria were the dominant bacteria in sediments. The most abundant taxa in the water samples were Proteobacteria, Actinobacteria, and Firmicutes, with Chloroplastida being the dominant eukaryote. Eukaryotes in sediments are much spatially stochastic. Function analysis showed that bacteria in the water column had more phototrophic genes than those in the sediment samples, while the latter had more nitrogen-transformation-involved genes. This suggested that river sediment is more active in the global nitrogen cycle, while the overlying water plays an important role in oxygenic photosynthesis.

The impacts of ocean acidification, warming and their interactive effects on coral prokaryotic symbionts

BackgroundReef-building corals, the foundation of tropical coral reefs, are vulnerable to climate change e.g. ocean acidification and elevated seawater temperature. Coral microbiome plays a key role in host acclimatization and maintenance of the coral holobiont’s homeostasis under different environmental conditions, however, the response patterns of coral prokaryotic symbionts to ocean acidification and/or warming are rarely known at the metatranscriptional level, particularly the knowledge of interactive and persistent effects is limited. Using branching Acropora valida and massive Galaxea fascicularis as models in a lab system simulating extreme ocean acidification (pH 7.7) and/or warming (32 °C) in the future, we investigated the changes of in situ active prokaryotic symbionts community and gene expression of corals under/after (6/9 d) acidification (A), warming (H) and acidification–warming (AH) by metatranscriptome analysis with pH8.1, 26 °C as the control.ResultsA, H and AH increased the relative abundance of in situ active pathogenic bacteria. Differentially expressed genes (DEGs) involved in virulence, stress resistance, and heat shock proteins were up-regulated. Many DEGs involved in photosynthesis, carbon dioxide fixation, amino acids, cofactors and vitamins, auxin synthesis were down-regulated. A broad array of new DEGs involved in carbohydrate metabolism and energy production emerged after the stress treatment. Different response patterns of prokaryotic symbionts of massive G. fascicularis and branching A. valida were suggested, as well as the interactive effects of combined AH and persistent effects.ConclusionsThe metatranscriptome-based study indicates that acidification and/or warming might change coral’s in situ active prokaryotic microbial diversity and functional gene expression towards more pathogenic and destabilized coral-microbes symbioses, particularly combined acidification and warming show interactive effects. These findings will aid in comprehension of the coral holobiont’s ability for acclimatization under future climate change.

Diversity of the Pacific Ocean coral reef microbiome

Coral reefs are among the most diverse ecosystems on Earth. They support high biodiversity of multicellular organisms that strongly rely on associated microorganisms for health and nutrition. However, the extent of the coral reef microbiome diversity and its distribution at the oceanic basin-scale remains to be explored. Here, we systematically sampled 3 coral morphotypes, 2 fish species, and planktonic communities in 99 reefs from 32 islands across the Pacific Ocean, to assess reef microbiome composition and biogeography. We show a very large richness of reef microorganisms compared to other environments, which extrapolated to all fishes and corals of the Pacific, approximates the current estimated total prokaryotic diversity for the entire Earth. Microbial communities vary among and within the 3 animal biomes (coral, fish, plankton), and geographically. For corals, the cross-ocean patterns of diversity are different from those known for other multicellular organisms. Within each coral morphotype, community composition is always determined by geographic distance first, both at the island and across ocean scale, and then by environment. Our unprecedented sampling effort of coral reef microbiomes, as part of the Tara Pacific expedition, provides new insight into the global microbial diversity, the factors driving their distribution, and the biocomplexity of reef ecosystems.

A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils.

Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.

Lemur Gut Microeukaryotic Community Variation Is Not Associated with Host Phylogeny, Diet, or Habitat.

Identifying the major forces driving variation in gut microbiomes enhances our understanding of how and why symbioses between hosts and microbes evolved. Gut prokaryotic community variation is often closely associated with host evolutionary and ecological variables. Whether these same factors drive variation in other microbial taxa occupying the animal gut remains largely untested. Here, we present a one-to-one comparison of gut prokaryotic (16S rRNA metabarcoding) and microeukaryotic (18S rRNA metabarcoding) community patterning among 12 species of wild lemurs. Lemurs were sampled from dry forests and rainforests of southeastern Madagascar and display a range of phylogenetic and ecological niche diversity. We found that while lemur gut prokaryotic community diversity and composition vary with host taxonomy, diet, and habitat, gut microeukaryotic communities have no detectable association with any of these factors. We conclude that gut microeukaryotic community composition is largely random, while gut prokaryotic communities are conserved among host species. It is likely that a greater proportion of gut microeukaryotic communities comprise taxa with commensal, transient, and/or parasitic symbioses compared with gut prokaryotes, many of which form long-term relationships with the host and perform important biological functions. Our study highlights the importance of greater specificity in microbiome research; the gut microbiome contains many "omes" (e.g., prokaryome, eukaryome), each comprising different microbial taxa shaped by unique selective pressures.

The soil microbiomes of forest ecosystems in Kenya: their diversity and environmental drivers

Soil microbiomes in forest ecosystems act as both nutrient sources and sinks through a range of processes including organic matter decomposition, nutrient cycling, and humic compound incorporation into the soil. Most forest soil microbial diversity studies have been performed in the northern hemisphere, and very little has been done in forests within African continent. This study examined the composition, diversity and distribution of prokaryotes in Kenyan forests top soils using amplicon sequencing of V4-V5 hypervariable region of the 16S rRNA gene. Additionally, soil physicochemical characteristics were measured to identify abiotic drivers of prokaryotic distribution. Different forest soils were found to have statistically distinct microbiome compositions, with Proteobacteria and Crenarchaeota taxa being the most differentially abundant across regions within bacterial and archaeal phyla, respectively. Key bacterial community drivers included pH, Ca, K, Fe, and total N while archaeal diversity was shaped by Na, pH, Ca, total P and total N. To contextualize the prokaryote diversity of Kenyan forest soils on a global scale, the sample set was compared to amplicon data obtained from forest biomes across the globe; displaying them to harbor distinct microbiomes with an over-representation of uncultured taxa such as TK-10 and Ellin6067 genera.

Biotechnological Potential of Hydrolytic Prokaryotic Component in Soils

The phylogenetic and functional diversity of a prokaryotic complex with biotechnological potential (carrying out the destruction of biopolymers, hydrocarbons; capable of synthesizing secondary metabolites; nitrogen fixation process) in soil and associated ecosystems has been studied. In order to identify the specifics of the development of metabolically active prokaryotes with biotechnological potential, the patterns of their distribution and the dependence of functional activity on the main environmental factors have been established. The study used molecular biological and bioinformatic approaches. The range of samples studied included modern soils (Volgograd, Tula, Moscow regions, Siberia and the Northern part of Central Kamchatka), relict habitats (Volgograd Region and Central Kamchatka) and permafrost soils of Antarctica (King George Island). The impact of anthropogenic and abiogenic loads on the development of the prokaryotic community was considered. In soils exposed to anthropogenic or abiogenic loads, along with a decrease in the diversity and abundance of prokaryotes, an increase in the number of genes marking the ability of a community to biodegradate xenobiotics, as well as genes encoding nitrogen transformations and the level of metabolism of cofactors and vitamins was found. The bacterial complex is capable of nitrification with high oil contamination of the soil, and its role also increases in the lower layers of the soil profile. Archaea play a leading role in the nitrification process in undisturbed soils. The revealed patterns indicate a high metabolic potential of the prokaryotic component of the objects under consideration and open up opportunities for biotechnological use of strains isolated from relict habitats.