Archaeal Communities Research Articles

The archaeome in metaorganism research, with a focus on marine models and their bacteria-archaea interactions.

Metaorganism research contributes substantially to our understanding of the interaction between microbes and their hosts, as well as their co-evolution. Most research is currently focused on the bacterial community, while archaea often remain at the sidelines of metaorganism-related research. Here, we describe the archaeome of a total of eleven classical and emerging multicellular model organisms across the phylogenetic tree of life. To determine the microbial community composition of each host, we utilized a combination of archaea and bacteria-specific 16S rRNA gene amplicons. Members of the two prokaryotic domains were described regarding their community composition, diversity, and richness in each multicellular host. Moreover, association with specific hosts and possible interaction partners between the bacterial and archaeal communities were determined for the marine models. Our data show that the archaeome in marine hosts predominantly consists of Nitrosopumilaceae and Nanoarchaeota, which represent keystone taxa among the porifera. The presence of an archaeome in the terrestrial hosts varies substantially. With respect to abundant archaeal taxa, they harbor a higher proportion of methanoarchaea over the aquatic environment. We find that the archaeal community is much less diverse than its bacterial counterpart. Archaeal amplicon sequence variants are usually host-specific, suggesting adaptation through co-evolution with the host. While bacterial richness was higher in the aquatic than the terrestrial hosts, a significant difference in diversity and richness between these groups could not be observed in the archaeal dataset. Our data show a large proportion of unclassifiable archaeal taxa, highlighting the need for improved cultivation efforts and expanded databases.

Climatic factors and fertilization rates co-regulate anaerobic methane oxidation driven by multiple electron acceptors in Chinese paddy fields

Paddy fields constitute a substantial anthropogenic reservoir of methane, with their inundation management fostering an ideal habitat for anaerobic methane oxidation. Within this context, a novel clade of anaerobic methanotrophic (ANME) archaea, known as ANME-2d, has been identified as capable of catalyzing anaerobic methane oxidation in conjunction with nitrate and metal oxide reduction processes within paddy fields. Nevertheless, our comprehension of the mechanisms governing anaerobic methane oxidation and its pivotal role in regulating methane emissions within rice paddies remains limited. This study quantified the rates of nitrate- and iron (III)-driven anaerobic methane oxidation through 13C-labeled stable isotope tracing experiments in Chinese paddy fields spanning diverse climate zones. Additionally, it investigated the ANME-2d archaeal community using quantitative polymerase chain reaction and high-throughput sequencing techniques. The nitrate-driven anaerobic methane oxidation contributed 10.9% to methane emission reduction. This contribution is equal to the previously identified contribution of nitrite-driven anaerobic methane oxidation (11.2%) mediated via NC10 bacteria, but played more important roles than iron-driven one (4.1%). The rates of nitrate- and nitrite-driven anaerobic methane oxidation differed significantly among climate zones and showed positive correlation with the mean annual temperature. Furthermore, their rates were more sensitive to temperature increases at higher and lower latitudes, respectively, under both representative concentration pathways 2.6 and 8.5. The rate of anaerobic methane oxidation driven by nitrate exhibited a positive correlation with nitrogen fertilization rate but displayed a negative correlation with phosphorus fertilization rate. Conversely, the rate of anaerobic methane oxidation driven by iron showed no significant correlation with either nitrogen or phosphorus fertilization rates. This study underscores the great potential of anaerobic methane oxidation in mitigating global warming, particularly under the conditions of future climate change and elevated nitrogen loading. These findings underline the necessity of incorporating anaerobic methane oxidation as a crucial parameter in methane emission prediction models.

Altered Gut Archaeal Communities in Anser erythropus Populations Wintering at Shengjin and Caizi Lakes in China

Altered Gut Archaeal Communities in Anser erythropus Populations Wintering at Shengjin and Caizi Lakes in China

Biogas upgrading by biotrickling filter: Effects of temperature and packing materials

Biological hydrogen-methane conversion technology can combine Power-to-Gas technology with biogas engineering and showed great potential in breaking through the limitations of both hydrogen storage and CO2 removal for biogas upgrading. However, the low gas–liquid mass transfer rate of hydrogen greatly limited its conversion efficiency and actual application. This study used a biotrickling filter (BTF) to address this limiting factor, and the effects of temperature and packing materials on hydrogen-methane conversion were investigated. Results showed that higher temperature was beneficial for hydrogen-methane conversion, and the highest conversion efficiency of 8.3 L/Lw·d was obtained at 55 °C with the archaeal community dominated by Methanothermobacter (99.97 %). The reactor using activated carbon as packing material showed the best hydrogen-methane conversion efficiency of 91.9 %, with the most methanogens fixed on the surface. Due to the electronic conductor property of activated carbon, the microbial communities of the biofilm were also different from the other two packing materials. Finally, the H2/CO2 ratio of the gas inflow was optimized, and the most suitable result was 2.5:1 (H2/CO2, v/v), which was far below the previously reported results and indicated higher efficiency in carbon dioxide removal. This study provided a promising way for biogas upgrading.

Effects of One-Step Abrupt Temperature Change on Anaerobic Co-Digestion of Kitchen Waste with Dewatered Sludge

The operating temperature of anaerobic digesters should be adjusted to adapt to seasonal variations in environmental temperature and the composition of organic solid waste. This study investigated the effects of one-step abrupt temperature changes (from mesophilic to thermophilic temperature, M–T, and from thermophilic to mesophilic temperature, T–M) and the inoculation ratio on methane yield and microbial diversity during the anaerobic co-digestion of kitchen waste with dewatered sludge. The results showed that the cumulative methane yield (CMY) level resulting from thermophilic control and the M–T digesters was greater than that resulting from mesophilic control and the T–M digesters. The CMF of M–T digesters increased, whereas the CMY of T–M digesters gradually decreased with an increase in the inoculation ratio. The maximal CMY was 385.1 mL/g-VSSadded, which corresponded to an M–T digester with a 5% inoculation ratio. In the later stage of anaerobic digestion, the bacterial community of T–M was more diverse than that of M–T, but the archaeal community of M–T was more diverse than that of T–M. The one-step temperature change from thermophilic to mesophilic temperature was more stable than that from mesophilic to thermophilic temperature.

Microbial adaptation to high ammonia environment in submerged anaerobic membrane bioreactor under volatile fatty acids and ammonia stresses

Anaerobic membrane bioreactor (AnMBR) is a high-rate bioreactor which is preferred over other configurations due to its potential to completely decouple solid retention time from hydraulic retention time. However, limited information is available on the bioreactor behavior under stressed environment, particularly during the startup period. The objective of this study was to investigate the effects of ammonium (NH4+) and organic loading rate (OLR) on the digestion performance and microbial population of submerged AnMBR. The findings revealed that high NH4+ was positively correlated with high methane concentration while high OLR increased methane production. The microbial analysis showed that both bacteria and archaea were influenced by the change of NH4+ and OLR. Particularly, at high OLR, Bacteroidetes were shown to be more sensitive to high NH4+ than Firmicutes, and Chloroflexi tolerated NH4+ even up to 2.5 g/L. Moreover, NH4+ was possibly the first driving factor in the change of methane production pathways from acetoclastic methanogenesis to hydrogenotrophic and methylotrophic methanogenesis. Membrane biofouling was also caused mainly by bacterial community (Firmicutes and Chloroflexi), while the contribution of archaeal community was minimal (Methanosaetaceae).

Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing

In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.

Equal importance of humic acids and nitrate in driving anaerobic oxidation of methane in paddy soils

Methane (CH4) is both generated and consumed in paddy soils, where anaerobic oxidation of methane (AOM) serves as a crucial process for mitigating CH4 emissions. Although the participation of humic acids (HA) and nitrate in AOM has been recognized, their relative roles and significance in paddy soils remain insufficiently investigated. In this study, we explored the potential activity of AOM driven by HA and nitrate, as well as the composition of archaeal communities in paddy soils across different rice growth periods and fertilization treatments. AOM activity ranged from 0.81 to 1.33 and 1.26 to 2.38 nmol of 13CO2 g−1 (dry soil) day−1 with HA and nitrate, respectively. No significant differences (p < 0.05) were observed between the AOM activity driven by HA and nitrate across the three fertilization treatments. According to AOM activity, the annual consumption of CH4 was estimated at approximately 0.49 ± 0.06 and 0.83 ± 0.19 Tg for AOM processes driven by HA and nitrate in Chinese paddy soils. Nitrate-driven AOM activity exhibited a positive (p < 0.05) correlation with the abundance of the ANME-2d mcrA gene but a negative (p < 0.05) correlation with the content of dissolved organic carbon. Intriguingly, HA-driven AOM activity was only correlated positively with the nitrate-driven AOM activity. Soil water content, soil organic carbon, nitrate and nitrite contents were significantly correlated with the relative abundance of methanogenic and methanotrophic archaea. These results identified the potential importance of HA and nitrate in driving AOM processes within paddy soils, providing a comprehensive understanding of the complex microbial processes regulating greenhouse gas emissions from paddy soils.

Composition of the rumen archaeal community of growing camels fed different concentrate levels.

Understanding the rumen fermentation and methanogenic community in camels fed intensively is critical for optimizing rumen fermentation, improving feed efficiency, and lowering methane emissions. Using Illumina MiSeq sequencing, quantitative real-time PCR, and high-performance liquid chromatography, this study evaluates the influence of different concentrate supplement levels in the diet on rumen fermentation as well as the diversity and structure of the rumen methanogenic community for growing dromedary camels. Twelve growing camels were divided into three groups and given three levels of concentrate supplement, 0.7% (C1), 1% (C2), and 1.3% (C3) based on their body weight. All animals were fed alfalfa hay ad libitum. The levels of total volatile fatty acid, rumen ammonia, and methanogen copy number were unaffected by the supplementation level. Increasing the concentrate supplement level increased the proportion of propionic acid while decreasing the proportion of acetic acid. Increasing the level of concentrate in the diet had no effect on alpha diversity metrics or beta diversity of rumen methanogens. Methanobrevibacter and Methanosphaera predominated the methanogenic community and were declined as concentrate supplement level increased. This study sheds new light on the effect of concentrate supplement level in growing camels' diet on rumen fermentation and methanogenic community, which could help in the development of a strategy that aimed to reduce methane emissions and enhance feed efficiency.

Insight into bacterial and archaeal community structure of Suaeda altissima and Suaeda dendroides rhizosphere in response to different salinity level.

Suaeda play an important ecological role in reclamation and improvement of agricultural saline soil due to strong salt tolerance. At present, research on Suaeda salt tolerance mainly focuses on the physiological and molecular regulation. However, the important role played by microbial communities in the high-salinity tolerance of Suaeda is poorly studied. Our findings have important implications for understanding the distribution patterns and the driving mechanisms of different Suaeda species and soil salinity levels. In addition, we explored the key microorganisms that played an important ecological role in Suaeda rhizosphere. We provide a basis for biological improvement and ecological restoration of salinity-affected areas.

Archaeal communities at gas-venting shallow basins in the northern Gulf of California (Wagner and Consag basins)

Deep-sea vents microorganisms have been well characterized with defined typical taxonomic groups, principally composed of archaea, while shallow hydrothermal vents are considered to host a different community with bacteria as predominant prokaryotes. This work focuses on two shallow basins in the northern Gulf of California: Wagner and Consag basins which show evidence of early stages of rifting processes and host numerous submarine vents with intense gas discharge. The exploratory study of archaea and bacteria in six sediment samples from the shallow vents in those basins (average depths of 100 m), demonstrate that similar archaea phyla inhabit these vents. The phylum Thermoproteota with Nitrosopumilus as the most abundant genera in five sites. However, in the sample with the highest temperature, the phylum Asgardarchaeota was predominant, and also the occurrence of archaeal lineages typical of deep sea vents like Nanoarchaeota, Thermoproteota, Euryarchaeota, and members from phylum Asgardarchaeota, were identified. This work is the first report of the presence of a typically deep vent community of archaea in this shallow vent environment.

Insights into the spatial distributions of bacteria, archaea, ammonia-oxidizing bacteria and archaea communities in sediments of Daya Bay, northern South China Sea

Microbe plays an important role in the biogeochemical cycles of the coastal waters. However, comprehensive information about the microbe in the gulf waters is lacking. This study employed high-throughput sequencing and quantitative PCR (qPCR) to investigate the distribution patterns of bacterial, archaeal, ammonia-oxidizing bacterial (AOB), and archaeal (AOA) communities in Daya Bay. Community compositions and principal coordinates analysis (PCoA) exhibited significant spatial characteristics in the diversity and distributions of bacteria, archaea, AOB, and AOA. Notably, various microbial taxa (bacterial, archaeal, AOB, and AOA) exhibited significant differences in different regions, playing crucial roles in nitrogen, sulfur metabolism, and organic carbon mineralization. Canonical correlation analysis (CCA) or redundancy analysis (RDA) indicated that environmental parameters such as temperature, salinity, nitrate, total nitrogen, silicate, and phosphate strongly influenced the distributions of bacterial, archaeal, AOB, and AOA. This study deepens the understanding of the composition and ecological function of prokaryotes in the bay.

Diversity and Functional Potential of Prokaryotic Communities in Depth Profile of Boreo-Nemoral Minerotrophic Pine Swamp (European Russia)

Natural peatlands represent a wide range of habitats that contribute to the conservation of biodiversity, including microbial biodiversity. Molecular biological methods make it possible to significantly increase the accounting of microbial diversity compared to the cultivation methods. The studies on microbial diversity in minerotrophic peatlands using molecular biological methods lag significantly behind such studies for ombrotrophic peatlands. In this work, we characterized the taxonomic composition and functional potential of the prokaryotic community of the minerotrophic pine swamp (fen) in the Tver region of northwestern Russia using high-throughput sequencing of 16S rRNA gene fragments. This study is unique, since it was carried out not in individual horizons but across the entire fen profile, taking into account the differentiation of the profile into the acrotelm and catotelm. The composition and dominants of bacterial and archaeal communities were determined not only at the level of phyla but also at the level of classes, families, and cultivated genera. The prokaryotic community of the studied fen was shown to have a high taxonomic diversity (28 bacterial and 10 archaeal phyla were identified). The profile differentiation of the taxonomic composition of prokaryotic communities is most clearly manifested in the analysis of the acrotelm and catotelm. In the bacterial communities of the acrotelm, the top three phyla included Acidobacteriota, Alphaproteobacteria, and Actinomycetota, in the catotelm—Betaproteobacteria, Bacteroidota, and Chloroflexota. In archaeal communities of the acrotelm, we discovered the monodominance of Nitrososphaerota, in the catotelm—the dominance of Bathyarchaeota and subdominance of Thermoplasmatota, Halobacterota, and Aenigmarchaeota. The hot spots of microbial diversity in the studied fen profile were found to be the 0–20 cm layer of the acrotelm and the 150–200 cm layer of the catotelm. In contrast to the taxonomic composition, the functional profiles of the prokaryotic communities of the acrotelm and catotelm were generally similar, except for methane metabolism, which was primarily carried out in the catotelm.

Effects of inocula on methane production and the microbial community in a rice straw anaerobic digestion system

Field experiments have shown that the mixed anaerobic digestion of straw with livestock and poultry manure can improve the efficiency of biogas production. We hypothesize that inoculation with livestock and poultry manure increase the efficiency of methane production by improving the diversity and structure of microbial community in the field anaerobic digestion system. In this study, an experimental system was established to simulate the microbial community of the mixed anaerobic digestion system in the field. The methane production and taxonomic composition of bacterial and archaeal communities in the rice straw anaerobic digestion systems were determined. We aim to reveal the effects of the inocula on the diversity and composition of bacterial and archaeal communities and the mechanism underlying the impact on biogas production in the field. The following results were obtained. (1) Inoculation significantly improved the efficiency of methane production in anaerobic digestion, and the best performance was achieved with treatment A (cleared biogas slurry), which obtained methane production that were 39.59 %, 106.85 %, and 123.00 % higher than in treatment B (pig manure extract), C (cleared biogas slurry + pig manure extract), and the control, respectively. (2) The inocula increased the abundance and diversity of bacterial communities in the early and middle stages and archaeal communities in the early stage. (3) The inocula also had a significant impact on bacterial and archaeal community composition in the early and middle stages. The inocula increased the relative abundance of Aquamicrobium_A, Proteiniphilum, and Cryptobacteroides but reduced the relative abundance of Macellibacteroides, Acinetobacter, and Phocaeicola. The dominant genus of archaeal community was altered from Methanosarcina to Methanocorpusculum. (4) It is concluded that inoculation significantly increase methane production as the inocula improve the abundance and diversity of bacteria and archaea of anaerobic digestion systems in the early and middle stages of digestion, as well as improve the structure and metabolic pathway of archaeal communities.

Tree and shrub richness modifies subtropical tree productivity by regulating the diversity and community composition of soil bacteria and archaea

BackgroundDeclines in plant biodiversity often have negative consequences for plant community productivity, and it becomes increasingly acknowledged that this may be driven by shifts in soil microbial communities. So far, the role of fungal communities in driving tree diversity-productivity relationships has been well assessed in forests. However, the role of bacteria and archaea, which are also highly abundant in forest soils and perform pivotal ecosystem functions, has been less investigated in this context. Here, we investigated how tree and shrub richness affects stand-level tree productivity by regulating bacterial and archaeal community diversity and composition. We used a landscape-scale, subtropical tree biodiversity experiment (BEF-China) where tree (1, 2, or 4 species) and shrub richness (0, 2, 4, 8 species) were modified.ResultsOur findings indicated a noteworthy decline in soil bacterial α-diversity as tree species richness increased from monoculture to 2- and 4- tree species mixtures, but a significant increase in archaeal α-diversity. Additionally, we observed that the impact of shrub species richness on microbial α-diversity was largely dependent on the level of tree species richness. The increase in tree species richness greatly reduced the variability in bacterial community composition and the complexity of co-occurrence network, but this effect was marginal for archaea. Both tree and shrub species richness increased the stand-level tree productivity by regulating the diversity and composition of bacterial community and archaeal diversity, with the effects being mediated via increases in soil C:N ratios.ConclusionsOur findings provide insight into the importance of bacterial and archaeal communities in driving the relationship between plant diversity and productivity in subtropical forests and highlight the necessity for a better understanding of prokaryotic communities in forest soils.-4HQdD_EuWHa-cff1NJXs2Video

Interplay between edaphic and climatic factors unravels plant and microbial diversity along an altitudinal gradient

Altitude influences biodiversity and physiochemical soil attributes in terrestrial ecosystems. It is of immense importance to know the patterns of how interactions among climatic and edaphic factors influence plant and microbial diversity in various ecosystems, particularly along the gradients. We hypothesize that altitudinal variation determines the distribution of plant and microbial species as well as their interactions. To test the hypothesis, different sites with variable altitudes were selected. Analyses of edaphic factors revealed significant (p < 0.001) effects of the altitude. Soil ammonium and nitrate were strongly affected by it contrary to potassium (K), soil organic matter and carbon. The response patterns of individual taxonomic groups differed across the altitudinal gradient. Plant species and soil fungal diversity increased with increasing altitude, while soil archaeal and bacterial diversity decreased with increasing altitude. Plant species richness showed significant positive and negative interactions with edaphic and climatic factors. Fungal species richness was also significantly influenced by the soil ammonium, nitrate, available phosphorus, available potassium, electrical conductivity, and the pH of the soil, but showed non-significant interactions with other edaphic factors. Similarly, soil variables had limited impact on soil bacterial and archaeal species richness along the altitude gradient. Proteobacteria, Ascomycota, and Thaumarchaeota dominate soil bacterial, fungal, and archaeal communities, with relative abundance of 27.4%, 70.56%, and 81.55%, respectively. Additionally, Cynodon dactylon is most abundant plant species, comprising 22.33% of the recorded plant taxa in various study sites. RDA revealed that these communities influenced by certain edaphic and climatic factors, e.g., Actinobacteria strongly respond to MAT, EC, and C/N ratio, Ascomycota and Basidiomycota show strong associations with EC and MAP, respectively. Thaumarcheota are linked to pH, and OM, while Cyperus rotundus are sensitive to AI and EC. In conclusion, the observed variations in microbial as well as plant species richness and changes in soil properties at different elevations provide valuable insights into the factors determining ecosystem stability and multifunctionality in different regions.

Pedological factors as drivers of archaeal and fungal communities in maize rhizosphere: a shotgun metagenomic sequencing approach

South Africa is a semi-arid country in need of soil conservation methods for sustainable agroecosystem practices. Over time, researchers have worked extensively on the plant growth beneficial effects of fungi. However, archaeal groups in the soil and rhizosphere of different plants are under-studied. The impact of soil edaphic factors on the community structure of archaeal and fungal groups in the maize rhizosphere is the focus of this research. This will confirm the hypothesis that environmental factors have a significant impact on the plant–soil rhizobiome. To achieve this objective, a shotgun metagenomics approach was used to analyze maize rhizosphere and bulk soils collected from North West and Gauteng provinces of South Africa. Our findings revealed that both the maize rhizosphere and bulk soils have several archaeal and fungal phyla in common. Besides, Ascomycota (30‒51%), Thaumarchaeota (14‒26%), Euryarchaeota (19‒29%), and Crenarchaeota (8‒12%) have significantly dominated the maize rhizosphere and surrounding bulk soils. In comparison, genera such as Nitrosopumilus (Ls-18.32%, Lc-16.25%; Rs-15.45%, Rc-11.47%), Candidatus Nitrososphaera (Ls-15.29%, Lc-13.37%; Rs-10.53%, Rc-8.29%), Cenarchaeum (Ls-8.84%, Lc-8.16%; Rs-7.63%, Rc-5.38%), Chaetomium (Ls-25.15%, Lc-23.05%; Rs-14.83%, Rc-6.29%), and Neurospora (Ls-2.09%, Lc-1.95%; Rs-1.05%, Rc-0.99%) were significantly higher in maize rhizosphere soils compared to bulk soils (p < 0.05). Diversity indices showed that the archaeal and fungal composition were significantly different across samples with the presence of unclassified groups that could indicate the possibility of novel organisms in the sampling areas. The forward selection of soil edaphic factors predicted N–NH4, pH, and organic matter as the major contributing factors to the variation in the fungal and archaeal communities. To fully exploit the advantages possessed by these species, it is necessary to better understand the main environmental factors driving microbial assemblages of the soil microbiome. In addition, mapping out a culture-based method to unveil the unclassified groups could assist in the discovery of biotechnologically important archaeal and fungal groups for sustainable plant growth.

Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf.

Kuwaiti territorial waters of the northwest Arabian Gulf represent a unique aquatic ecosystem prone to various environmental and anthropogenic stressors that pose significant constraints on the resident biota which must withstand extreme temperatures, salinity levels, and reducing conditions, among other factors to survive. Such conditions create the ideal environment for investigations into novel functional genetic adaptations of resident organisms. Firstly, however, it is essential to identify said organisms and understand the dynamic nature of their existence. Thus, this study provides the first comprehensive analysis of bacterial and archaeal community structures in the unique waters of Kuwait located in the Northwest Arabian Gulf and analyzes their variations with respect to depth, season, and location, as well as their susceptibility to changes in abundance with respect to various physicochemical parameters. Importantly, this study is the first of its kind to utilize a shotgun metagenomics approach with sequencing performed at an average depth of 15 million paired end reads per sample, which allows for species-level community profiling and sets the framework for future functional genomic investigations. Results showed an approximately even abundance of both archaeal (42.9%) and bacterial (57.1%) communities, but significantly greater diversity among the bacterial population, which predominantly consisted of members of the Proteobacteria, Cyanobacteria, and Bacteroidetes phyla in decreasing order of abundance. Little to no significant variations as assessed by various metrics including alpha and beta diversity analyses were observed in the abundance of archaeal and bacterial populations with respect to depth down the water column. Furthermore, although variations in differential abundance of key genera were detected at each of the three sampling locations, measurements of species richness and evenness revealed negligible variation (ANOVA p<0.05) and only a moderately defined community structure (ANOSIM r2 = 0.243; p>0.001) between the various locations. Interestingly, abundance of archaeal community members showed a significant increase (log2 median ratio of RA = 2.6) while the bacterial population showed a significant decrease (log2 median ratio = -1.29) in the winter season. These findings were supported by alpha and beta diversity analyses as well (ANOSIM r2 = 0.253; p>0.01). Overall, this study provides the first in-depth analysis of both bacterial and archaeal community structures developed using a shotgun metagenomic approach in the waters of the Northwest Arabian Gulf thus providing a framework for future investigations of functional genetic adaptations developed by resident biota attempting to survive in the uniquely extreme conditions to which they are exposed.

Habitat-related variability in the morphological and taxonomic diversity of microbial communities in two Hungarian epigenic karst caves.

The physical and chemical characteristics of the bedrock, along with the geological and hydrological conditions of karst caves may influence the taxonomic and functional diversity of prokaryotes. Most studies so far have focused on microbial communities of caves including only a few samples and have ignored the chemical heterogeneity of different habitat types such as sampling sites, dripping water, carbonate precipitates, cave walls, cave sediment and surface soils connected to the caves. The aim of the present study was to compare the morphology, the composition and physiology of the microbiota in caves with similar environmental parameters (temperature, host rock, elemental and mineral composition of speleothems) but located in different epigenic karst systems. Csodabogyós Cave and Baradla Cave (Hungary) were selected for the analysis of bacterial and archaeal communities using electron microscopy, amplicon sequencing, X-ray diffraction, and mass spectroscopic techniques. The microbial communities belonged to the phyla Pseudomonadota, Acidobacteriota, Nitrospirota and Nitrososphaerota, and they showed site-specific variation in composition and diversity. The results indicate that morphological and physiological adaptations provide survival for microorganisms according to the environment. In epigenic karst caves, prokaryotes are prone to increase their adsorption surface, cooperate in biofilms, and implement chemolithoautotrophic growth with different electron-donors and acceptors available in the microhabitats.

Deciphering microbiomes dozens of meters under our feet and their edaphoclimatic and spatial drivers.

Microbes inhabiting deep soil layers are known to be different from their counterpart in topsoil yet remain under investigation in terms of their structure, function, and how their diversity is shaped. The microbiome of deep soils (>1 m) is expected to be relatively stable and highly independent from climatic conditions. Much less is known, however, on how these microbial communities vary along climate gradients. Here, we used amplicon sequencing to investigate bacteria, archaea, and fungi along fifteen 18-m depth profiles at 20-50-cm intervals across contrasting aridity conditions in semi-arid forest ecosystems of China's Loess Plateau. Our results showed that bacterial and fungal α diversity and bacterial and archaeal community similarity declined dramatically in topsoil and remained relatively stable in deep soil. Nevertheless, deep soil microbiome still showed the functional potential of N cycling, plant-derived organic matter degradation, resource exchange, and water coordination. The deep soil microbiome had closer taxa-taxa and bacteria-fungi associations and more influence of dispersal limitation than topsoil microbiome. Geographic distance was more influential in deep soil bacteria and archaea than in topsoil. We further showed that aridity was negatively correlated with deep-soil archaeal and fungal richness, archaeal community similarity, relative abundance of plant saprotroph, and bacteria-fungi associations, but increased the relative abundance of aerobic ammonia oxidation, manganese oxidation, and arbuscular mycorrhizal in the deep soils. Root depth, complexity, soil volumetric moisture, and clay play bridging roles in the indirect effects of aridity on microbes in deep soils. Our work indicates that, even microbial communities and nutrient cycling in deep soil are susceptible to changes in water availability, with consequences for understanding the sustainability of dryland ecosystems and the whole-soil in response to aridification. Moreover, we propose that neglecting soil depth may underestimate the role of soil moisture in dryland ecosystems under future climate scenarios.