Prokaryotic Composition Research Articles

Anthropogenic activities affect the diverse autotrophic communities of coastal sediments

Coastal sediments are a critical domain for carbon sequestration and are profoundly impacted by human activities. Therefore, it is essential to understand the structure and components of benthic autotrophs that play a crucial role in carbon sequestration processes, as well as the influence of anthropogenic activities on their communities. This study utilized an urban estuary, an industrial sea bay, a maricultural sea region, and two mangrove coastlines within the coastal areas of Guangdong Province, China. The micro-benthos in these environments, including prokaryotes and eukaryotes, were identified through high-throughput sequencing of 16S rRNA and 18S rRNA genes. The findings show that the autotrophic composition was altered by the interactions of anthropogenic heavy metals (Cd and Zn) and micro-eukaryotes (protazoa, metazoa, and parasitic organisms). Industrial pollution reduced the abundance of both prokaryotic and eukaryotic autotrophs. Mangroves induced a substantial transformation in the sediment eukaryotic and prokaryotic composition, increasing the proportion of autotrophs, notably sulfur-oxidizing and iron-oxidizing bacteria and microalgae. This alteration suggests an increase in specific sulfur and iron cycling with simultaneous carbon sequestration within mangrove sediments. These results indicate that anthropogenic activities affect sediment carbon sequestration by altering autotrophic assemblages along coastlines, thereby inducing consequential shifts in overall elemental cycling processes.

Estimating taxonomic and functional structure along a tropical estuary: linking metabolic traits and aspects of ecosystem functioning.

Microbial life forms are among the most ubiquitous on Earth, yet many remain understudied in Caribbean estuaries. We report on the prokaryote community composition of the Urabá Estuary in the Colombian Caribbean using 16S rRNA gene-transcript sequencing. We also assessed potential functional diversity through 38 metabolic traits inferred from 16S rRNA gene data. Water samples were collected from six sampling stations at two depths with contrasting light-penetration conditions along an approximately 100 km transect in the Gulf of Urabá in December 2019. Non-metric multidimensional scaling analysis grouped the samples into two distinct clusters along the transect and between depths. The primary variables influencing the prokaryote community composition were the sampling station, depth, salinity, and dissolved oxygen levels. Twenty percent of genera (i.e., 58 out 285) account for 95% of the differences between groups along the transect and among depths. All of the 38 metabolic traits studied showed some significant relationship with the tested environmental variables, especially salinity and except with temperature. Another non-metric multidimensional scaling analysis, based on community-weighted mean of traits, also grouped the samples in two clusters along the transect and over depth. Biodiversity facets, such as richness, evenness, and redundancy, indicated that environmental variations-stemming from river discharges-introduce an imbalance in functional diversity between surface prokaryote communities closer to the estuary's head and bottom communities closer to the ocean. Our research broadens the use of 16S rRNA gene transcripts beyond mere taxonomic assignments, furthering the field of trait-based prokaryote community ecology in transitional aquatic ecosystems.IMPORTANCEThe resilience of a dynamic ecosystem is directly tied to the ability of its microbes to navigate environmental gradients. This study delves into the changes in prokaryote community composition and functional diversity within the Urabá Estuary (Colombian Caribbean) for the first time. We integrate data from 16S rRNA gene transcripts (taxonomic and functional) with environmental variability to gain an understanding of this under-researched ecosystem using a multi-faceted macroecological framework. We found that significant shifts in prokaryote composition and in primary changes in functional diversity were influenced by physical-chemical fluctuations across the estuary's environmental gradient. Furthermore, we identified a potential disparity in functional diversity. Near-surface communities closer to the estuary's head exhibited differences compared to deeper communities situated farther away. Our research serves as a roadmap for posing new inquiries about the potential functional diversity of prokaryote communities in highly dynamic ecosystems, pushing forward the domain of multi-trait-based prokaryote community ecology.

Activated sludge prokaryote and eukaryote characterization in a pulp mill facility using amplicon sequencing

The pulp and paper industry, a major global sector, supports economies and jobs while contributing to various products. While providing valuable products, and despite Best Available Techniques (BAT) being used, managing wastewater effectively remains a key area for developing technologies and alternatives for environmental protection. Activated sludge (AS) systems are commonly used for effluent treatment, where microorganisms composition influences reactor efficiency. Current monitoring strategies show limited correlation with chemical parameters. Metabarcoding, a DNA sequencing approach, offers a promising alternative to profile microbial communities comprehensively. Utilizing MinION and Illumina sequencing, this study reveals the prokaryotic and eukaryotic microbial communities in AS from an extended aeration-activated sludge reactor from a pulp mill for the first time. Eukaryotic composition evaluated by 18S amplicon sequencing revealed Protists as the dominant group, followed by Animalia and Fungi. Within these groups, the most abundant phyla detected were Ciliophora (75 % on average), Rotifera (90 % on average), and Cryptomycota (60 % on average), respectively. Genera like Prorodon and Limnias stand out due to their high relative abundance within the Protist and Animalia group, respectively. A comparative analysis with routine microorganism composition assessment by microscopy revealed consistent taxonomic trends, affirming the feasibility of amplicon sequencing for routine microbial community surveillance. Furthermore, the incorporation of metabarcoding enhanced the depth of results. Prokaryotic composition analyzed by 16S amplicon sequencing revealed microorganisms previously described as relevant to the wastewater treatment process but highlighted dominant specific groups even when compared to other pulp facilities. Genera like Terrimonas, Defluviicoccus, and Methylocaldum appear as the most abundant among the identified genera. For proper reactor operation, microorganisms must aggregate around organic matter in flocs, which reflect reactor health and are composed of 5 % eukaryotes and 95 % prokaryotes. Hence, the characterization of both groups of microorganisms is crucial. Differences in communities between the wastewater treatment plant's aeration zones emphasize the importance of comprehensive community characterization. The study underscores metabarcoding's potential as a monitoring tool, for future linking of microbial communities with process patterns for improved environmental management in the pulp and paper industry and emphasizes the importance of establishing unique baselines for microbial communities in activated sludge systems.

Metataxonomic and metabolomic profiling revealed Pinus koraiensis cone essential oil reduced methane emission through affecting ruminal microbial interactions and host-microbial metabolism

BackgroundPinus koraiensis cone essential oil (PEO) contains functional compounds such as monoterpene hydrocarbons, and the administration of PEO reduced methane (CH4) emissions during growing phase of goats. However, the mode of action of PEO driven CH4 reduction is not known, especially how the administration of PEO can affect rumen microbiota and host metabolism in goats during the fattening phase. This study aimed to elucidate the potential microbial and host responses PEO supplementation in goats using metataxonomics (prokaryotes and protozoa) and metabolomics (rumen fluid and serum).ResultsTen fattening Korean native goats were divided into two dietary groups: control (CON; basal diet without additives) and PEO (basal diet + 1.5 g/d of PEO) with a 2 × 2 crossover design and the treatment lasted for 11 weeks. Administration of PEO reduced CH4 concentrations in the exhaled gas from eructation by 12.0–13.6% (P < 0.05). Although the microbial composition of prokaryotes (bacteria and archaea) and protozoa in the rumen was not altered after PEO administration. MaAsLin2 analysis revealed that the abundance of Selenomonas, Christensenellaceae R-7 group, and Anaerovibrio were enriched in the rumen of PEO supplemented goats (Q < 0.1). Co-occurrence network analysis revealed that Lachnospiraceae AC2044 group and Anaerovibrio were the keystone taxa in the CON and PEO groups, respectively. Methane metabolism (P < 0.05) was enriched in the CON group, whereas metabolism of sulfur (P < 0.001) and propionate (P < 0.1) were enriched in the PEO group based on microbial predicted functions. After PEO administration, the abundance of 11 rumen and 4 serum metabolites increased, whereas that of 25 rumen and 14 serum metabolites decreased (P < 0.1). Random forest analysis identified eight ruminal metabolites that were altered after PEO administration, among which four were associated with propionate production, with predictive accuracy ranging from 0.75 to 0.88. Additionally, we found that serum sarcosine (serum metabolite) was positively correlated with CH4 emission parameters and abundance of Methanobrevibacter in the rumen (|r|≥ 0.5, P < 0.05).ConclusionsThis study revealed that PEO administration reduced CH4 emission from of fattening goats with altered microbial interactions and metabolites in the rumen and host. Importantly, PEO administration affected utilizes various mechanisms such as formate, sulfur, methylated amines metabolism, and propionate production, collectively leading to CH4 reduction. The knowledge is important for future management strategies to maintain animal production and health while mitigate CH4 emission.

Sponge-associated microbes in the twilight zone of Curaçao

Mesophotic reefs, located in the "Twilight Zone" of the ocean, are coral reefs that exist in relatively deep waters ranging from approximately 30 to 150 m below the surface. These reefs are situated just beyond the reach of conventional SCUBA diving and are typically explored using advanced diving techniques or with the aid of submersibles. In the present study, we used a state-of-the-art submersible to sample 26 sponge specimens belonging to 11 species. High (HMA) or low (LMA) microbial abundance status was assigned to species based on TEM imagery. Prokaryotic communities associated with these sponges were, furthermore, assessed using high-throughput sequencing. Proteobacteria, Chloroflexi, Actinobacteriota, and Acidobacteriota were the most abundant phyla overall. HMA/LMA status proved to be a highly significant predictor of prokaryotic composition. HMA sponges also tended to be more diverse in terms of richness and evenness than LMA sponges. 14 predictor-classes were identified using an exploratory technique based on machine learning including classes within the phyla Chloroflexi (e.g., Dehalococcoidia and JG30-KF-CM66) and Acidobacteriota (Thermoanaerobaculia and Subgroups 11 and 21). Previous studies have demonstrated the prevalence of the HMA/LMA dichotomy in shallow waters and, recently, the deep sea. Our results demonstrate its prevalence in the mesophotic realm.

Prokaryotic community assembly patterns and nitrogen metabolic potential in oxygen minimum zone of Yangtze Estuary water column

It is predicted that oxygen minimum zones (OMZs) in the ocean will expand as a consequence of global warming and environmental pollution. This will affect the overall microbial ecology and microbial nitrogen cycle. As one of the world's largest alluvial estuaries, the Yangtze Estuary has exhibited a seasonal OMZ since the 1980s. In this study, we have uncovered the microbial composition, the patterns of community assembly and the potential for microbial nitrogen cycling within the water column of the Yangtze Estuary, with a particular focus on OMZ. Based on the 16 S rRNA gene sequencing, a specific spatial variation in the composition of prokaryotic communities was observed for each water layer, with the Proteobacteria (46.1%), Bacteroidetes (20.3%), and Cyanobacteria (10.3%) dominant. Stochastic and deterministic processes together shaped the community assembly in the water column. Further, pH was the most important environmental factor influencing prokaryotic composition in the surface water, followed by silicate, PO43−, and distance offshore (p < 0.05). Water depth, NH4+, and PO43− were the main factors in the bottom water (p < 0.05). At last, species analysis and marker gene annotation revealed candidate nitrogen cycling performers, and a rich array of nitrogen cycling potential in the bottom water of the Yangtze Estuary. The determined physiochemical parameters and potential for nitrogen respiration suggested that organic nitrogen and NO3− (or NO2−) are the preferred nitrogen sources for microorganisms in the Yangtze Estuary OMZ. These findings are expected to advance research on the ecological responses of estuarine oxygen minimum zones (OMZs) to future global climate perturbations.

Convergence effect during spatiotemporal succession of lacustrine plastisphere: loss of priority effects and turnover of microbial species.

Succession is a fundamental aspect of ecological theory, but studies on temporal succession trajectories and ecological driving mechanisms of plastisphere microbial communities across diverse colonization environments remain scarce and poorly understood. To fill this knowledge gap, we assessed the primary colonizers, succession trajectories, assembly, and turnover mechanisms of plastisphere prokaryotes and eukaryotes from four freshwater lakes. Our results show that differences in microbial composition similarity, temporal turnover rate, and assembly processes in the plastisphere do not exclusively occur at the kingdom level (prokaryotes and eukaryotes), but also depend on environmental conditions and colonization time. Thereby, the time of plastisphere colonization has a stronger impact on community composition and assembly of prokaryotes than eukaryotes, whereas for environmental conditions, the opposite pattern holds true. Across all lakes, deterministic processes shaped the assembly of the prokaryotes, but stochastic processes influenced that of the eukaryotes. Yet, they share similar assembly processes throughout the temporal succession: species turnover over time causes the loss of any priority effect, which leads to a convergent succession of plastisphere microbial communities. The increase and loss of microbial diversity in different kingdoms during succession in the plastisphere potentially impact the stability of entire microbial communities and related biogeochemical cycles. Therefore, research needs to integrate temporal dynamics along with spatial turnovers of the plastisphere microbiome. Taking the heterogeneity of global lakes and the diversity of global climate patterns into account, we highlight the urgency to investigate the spatiotemporal succession mechanism of plastisphere prokaryotes and eukaryotes in more lakes around the world.

The Vertical Metabolic Activity and Community Structure of Prokaryotes along Different Water Depths in the Kermadec and Diamantina Trenches.

Prokaryotes play a key role in particulate organic matter's decomposition and remineralization processes in the vertical scale of seawater, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity of the vertical distribution in the trenches. The composition and distribution of prokaryotes in the water columns and benthic boundary layers of the Kermadec Trench and the Diamantina Trench were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog EcoplateTM microplates culture to analyze the microbial metabolic activity. Microbial communities in both trenches were dominated by Nitrososphaera and Halobacteria in archaea, and by Alphaproteobacteria and Gammaproteobacteria in bacteria, and the microbial community structure was significantly different between the water column and the benthic boundary layer. At the surface water, amino acids and polymers were used preferentially; at the benthic boundary layers, amino acids and amines were used preferentially. Cooperative relationships among different microbial groups and their carbon utilization capabilities could help to make better use of various carbon sources along the water depths, reflected by the predominantly positive relationships based on the co-occurrence network analysis. In addition, the distinct microbial metabolic activity detected at 800 m, which was the lower boundary of the twilight zone, had the lowest salinity and might have had higher proportions of refractory carbon sources than the shallower water depths and benthic boundary layers. This study reflected the initial preference of the carbon source by the natural microbes in the vertical scale of different trenches and should be complemented with stable isotopic tracing experiments in future studies to enhance the understanding of the complex carbon utilization pathways along the vertical scale by prokaryotes among different trenches.

Plant colonizers of a mercury contaminated site: trace metals and associated rhizosphere bacteria

Background and aimsMercury (Hg) contamination poses severe human and environmental health risks. We aimed to evaluate the colonization of Hg-contaminated sites by native plants and the prokaryotic composition of rhizosphere soil communities of the dominant plant species.MethodsA field study was conducted at a Hg-contaminated site in Romania. Metal concentrations in soil and plant samples were analyzed using portable X-ray fluorescence spectrometry. The prokaryotic composition of rhizosphere soil communities was determined through 16S rRNA amplicon sequencing and community functionality was predicted through PICRUSt2.ResultsSite-specific trace metal distribution across the site drove plant species distribution in the highly contaminated soil, with Lotus tenuis and Diplotaxis muralis associated with higher Hg concentrations. In addition, for the bacterial communities in the rhizosphere soil of D. muralis, there was no observable decrease in alpha diversity with increasing soil Hg levels. Notably, Actinomycetota had an average of 24% relative abundance in the rhizosphere communities that also tested positive for the presence of merA, whereas in the absence of merA the phylum’s relative abundance was approximately 2%. merA positive rhizosphere communities also displayed an inferred increase in ABC transporters.ConclusionsThe results suggest a dependence of species-wise plant survival on local trace metal levels in soil, as well as an intricate interplay of the latter with rhizosphere bacterial diversity. Knowledge of these interdependencies could have implications for phytoremediation stakeholders, as it may allow for the selection of plant species and appropriate soil microbial inoculates with elevated Hg tolerance.

Prokaryote Composition and Structure of Rumen Fluid before and after In Vitro Rumen Fermentation

Background: This study aimed to investigate the impact of in vitro rumen fermentation (IVRF) on the microbiome structure and composition of rumen fluid before and after fermentation assays. Methods and Results: Six separate fermentation batches were run for 48 h using maize silage as the basal feed. Rumen fluid samples were analyzed before (RF; only rumen fluid inoculant) and after 48 h fermentation assay (MS; maize silage as the substrate) and further processed for microbiome analysis using amplicon sequencing targeting the V4 region of the bacterial 16S rRNA gene. Bacterial alpha diversity revealed that the Shannon index and observed index were similar between MS and RF fluid. The core microbiome was detected in 88.6% of the amplicon sequence variants in MS and RF. Taxonomic analysis at the phylum level showed similar abundances of Bacteroidetes, Proteobacteria, Firmicutes, Verrucomicrobiota, Spirochaetota, Patescibacteria, and Campilobacterota in MS and RF. The Bray–Curtis distance matrix showed similar bacterial community structure among MS and RF samples. Conclusion: Our results indicated that the in vitro procedure did not affect the bacterial community structure compared to the original rumen fluid inoculum. It should be noted that assessing the microbiome at a single endpoint (i.e., 48 h) may not provide a comprehensive understanding of the microbiome profile dynamics. However, the findings of this study provide a basis for future microbiome-based in vitro fermentation tests and confirm that the technique allows a high degree of species diversity that approximates the rumen function in vivo.

Responses of microbial communities subjected to hydrodynamically induced disturbances in an organic contaminated site

Organic contaminated sites have gained significant attention as a prominent contributor to shallow groundwater contamination. However, limited knowledge exists regarding the impact of hydrodynamic effects on microbially mediated contaminant degradation at such sites. In this study, we investigated the distribution characteristics and community structure of prokaryotic microorganisms at the selected site during both wet and dry seasons, with a particular focus on their environmental adaptations. The results revealed significant seasonal variations (P < 0.05) in the α-diversity of prokaryotes within groundwater. The dry season showed more exclusive OTUs than the wet season. The response of prokaryotic metabolism to organic pollution pressure in different seasons was explored by PICRUSt2, and enzymes associated with the degradation of organic pollutants were identified based on the predicted functions. The results showed that hormesis was considered as an adaptive response of microbial communities under pollution stress. In addition, structural equation models demonstrated that groundwater level fluctuations can, directly and indirectly, affect the abundance and diversity of prokaryotes through other factors such as oxidation reduction potential (ORP), dissolved oxygen (DO), and naphthalene (Nap). Overall, our findings imply that the taxonomic composition and functional properties of prokaryotes in groundwater in organic contaminated sites is influenced by the interaction between seasonal variations and characteristics of organic pollution. The results provide new insights into microbiological processes in groundwater systems in organic contaminated sites.

Merging and concatenation of sequencing reads: a bioinformatics workflow for the comprehensive profiling of microbiome from amplicon data.

A comprehensive profiling of microbial diversity is essential to understand the ecosystem functions. Universal primer sets such as the 515Y/926R could amplify a part of 16S and 18S rRNA and infer the diversity of prokaryotes and eukaryotes. However, the analyses of mixed sequencing data pose a bioinformatics challenge; the 16S and 18S rRNA sequences need to be separated first and analysed individually/independently due to variations in the amplicon length. This study describes an alternative strategy, a merging and concatenation workflow, to analyse the mixed amplicon data without separating the 16S and 18S rRNA sequences. The workflow was tested with 24 mock community (MC) samples, and the analyses resolved the composition of prokaryotes and eukaryotes adequately. In addition, there was a strong correlation (cor=0.950; P-value=4.754e-10) between the observed and expected abundances in the MC samples, which suggests that the computational approach could infer the microbial proportions accurately. Further, 18 samples collected from the Sundarbans mangrove region were analysed as a case study. The analyses identified Proteobacteria, Bacteroidota, Actinobacteriota, Cyanobacteria, and Crenarchaeota as dominant bacterial phyla and eukaryotic divisions such as Metazoa, Gyrista, Cryptophyta, Chlorophyta, and Dinoflagellata were found to be dominant in the samples. Thus, the results support the applicability of the method in environmental microbiome research. The merging and concatenation workflow presented here requires considerably less computational resources and uses widely/commonly used bioinformatics packages, saving researchers analyses time (for equivalent sample numbers, compared to the conventional approach) required to infer the diversity of major microbial domains from mixed amplicon data at comparable accuracy.

An exploratory study of sponges, sponge-associated, and planktonic prokaryotic communities in an artificial coral reef environment

Abstract In the present study, we assessed the sponge fauna, sponge-associated, and planktonic prokaryotic communities residing in Burgers' Zoo Ocean aquarium, Arnhem, the Netherlands. The Ocean aquarium consisted of separate displays and life support systems, and included fish-only systems in addition to a large, 750,000 L tank containing a living, tropical coral reef ecosystem. Sponges were observed throughout the aquarium system and were identified as belonging to the genera Chalinula, Chondrilla, Chondrosia, Cinachyrella, Stylissa, Suberites and Tethya. There was a highly significant difference in composition between sponge-associated and planktonic prokaryotic communities. The tanks in which the sponges were sampled appeared to have a secondary structural effect on prokaryotic composition with sponges and water from the same tanks sharing several microorganisms. Both sponge-associated and planktonic prokaryotic communities housed prokaryotic taxa, which were highly similar to microorganisms previously recorded in sponges or coral reef environments, including taxa potentially involved in nitrification, denitrification, sulphur oxidation, and antibiotic biosynthesis. Several abundant microorganisms were only recorded in sponges and these may play a role in maintaining water quality in the aquarium system. Potential pathogens, e.g. related to Photobacterium damselae, and beneficial organisms, e.g. related to Pseudovibrio denitrificans, were also detected. The present study showed that Burgers' Zoo Ocean aquarium housed diverse free-living and host-associated prokaryotic communities. Future research should focus on identifying conditions and microbial communities conducive to a healthy aquarium environment.

Impact of wildfire ash on bacterioplankton abundance and community composition in a coastal embayment (Ría de Vigo, NW Spain)

Wildfire ash can have an impact on coastal prokaryotic plankton. To understand the extent to which community composition and abundance of coastal prokaryotes are affected by ash, two ash addition experiments were performed. Ash from a massive wildfire that took place in the Ría de Vigo watershed in October 2017 was added to natural surface water samples collected in the middle sector of the ría during the summer of 2019 and winter of 2020, and incubated for 72 h, under natural water temperature and irradiance conditions. Plankton responses were assessed through chlorophyll a and bacterial abundance measurements. Prokaryotic DNA was analyzed using 16S rRNA gene partial sequencing. In summer, when nutrient concentrations were low in the ría, the addition of ash led to an increase in phytoplankton and bacterial abundance, increasing the proportions of Alteromonadales, Flavobacteriales, and the potentially pathogenic Vibrio, among other taxa. After the winter runoff events, nutrient concentrations in the Ría de Vigo were high, and only minor changes in bacterial abundance were detected. Our findings suggest that the compounds associated with wildfire ash can alter the composition of bacterioplanktonic communities, which is relevant information for the management of coastal ecosystems in fire-prone areas.

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.

Profiling Prokaryotic Communities and Aaptamines of Sponge Aaptos suberitoides from Tulamben, Bali.

Sponges (Porifera) harbor a diversity of microorganisms that contribute largely to the production a vast array of bioactive compounds. The microorganisms associated with sponge have an important impact on the chemical diversity of the natural products. Herein, our study focuses on an Aaptos suberitoides commonly found in Indonesia. The objective of this study was to investigate the profile of prokaryotic community and the presence of aaptamine metabolites in sponge Aaptos suberitoides. Sponges were collected from two site locations (Liberty Wreck and Drop Off) in Tulamben, Bali. The sponges were identified by barcoding DNA cytochrome oxidase subunit I (COI) gene. The profile of prokaryotic composition was investigated by amplifying the 16S rRNA gene using primers 515f and 806r to target the V4 region. The metabolites were analyzed using LC-MS, and dereplication was done to identify the aaptamines and its derivates. The barcoding DNA of the sponges confirmed the identity of samples as Aaptos suberitoides. The prokaryotic communities of samples A. suberitoides were enriched and dominated by taxa Proteobacteria, Chloroflexi, Actinobacteria, and Acidobacteria. The chemical analysis showed that all sponges produce aaptamine and isoaaptamine except A. suberitoides S2421 produce analog of aaptamines. This is the first report on the profile of prokaryotic community and the aaptamine of tropical marine sponges, A. suberitoides, from Tulamben, Bali.

Networks of mineral-associated organic matter fractions in forest ecosystems

Mineral-associated organic matter (MAOM), the largest soil carbon pool, is formed through a series of organo-mineral interaction mechanisms. However, different organo-mineral fractions relevant to specific stabilization mechanisms and their response to environmental variables are poorly understood, which hinders accurate prediction of MAOM preservation under climate change. We applied sequential chemical extraction to separate MAOM into different organo-mineral fractions. To assess of response of different organo-mineral fractions to climate change, alpine forest soils with high environmental sensitivity along a controlled environmental gradient were selected. Residual OM and weakly adsorbed OM were the primary organo-mineral fractions, accounting for approximately 45.1–67.7 % and 16.4–30.6 %, respectively, of the total organic carbon (TOC). Climate exerted considerable indirect effects on the preservation of organo-mineral fractions through weathering and edaphic and biotic variables. Moreover, organo-mineral fractions were closely associated with metal cations (mainly Fe3+/Al3+) and secondary minerals, forming complex networks. Water-soluble OM (WSOM), weakly adsorbed OM and Fe/Al oxyhydroxides-stabilized OM were tightly linked, occupying the central position of the networks, and were closely related to soil pH, moisture and prokaryotic composition, indicating that edaphic and biotic factors might play important roles in maintaining the network structure and topology. In addition, Fe/Al-OM complexes, oxyhydroxides-stabilized OM and residual OM in the network were greatly impacted by climate and weathering factors, including precipitation, temperature and the plagioclase index of alteration (PIA). The complex network among organo-mineral fractions sheds light on MAOM dynamic stabilization for better predicting MAOM preservation under climate change.

Soybean and Cotton Spermosphere Soil Microbiome Shows Dominance of Soilborne Copiotrophs.

The spermosphere is the transient, immediate zone of soil around imbibing and germinating seeds. It represents a habitat where there is contact between seed-associated microbes and soil microbes, but it is studied less than other plant habitats. Previous studies on spermosphere microbiology were primarily culture based or did not sample the spermosphere soil as initially defined in space and time. Thus, the objectives of this study were to develop an efficient strategy to collect spermosphere soils around imbibing soybean and cotton in nonsterile soil and investigate changes in microbial communities. The method employed sufficiently collected spermosphere soil as initially defined in space by constraining the soil sampled with a cork borer and confining the soil to a 12-well microtiter plate. Spermosphere prokaryote composition changed over time and depended on the crop within 6 h after seeds were sown. By 12 to 18 h, crops had unique microbial communities in spermosphere soils. Prokaryote evenness dropped following seed imbibition, with the proliferation of copiotrophic soil bacteria. Due to their long history of plant growth promotion, prokaryote operational taxonomic units (OTUs) in Bacillus, Paenibacillus, Burkholderia, Massilia, Azospirillum, and Pseudomonas were notable organisms enriched. Fungi and prokaryotes were hub taxa in cotton and soybean spermosphere networks. Additionally, the enriched taxa were not hubs in networks, suggesting that other taxa besides those enriched may be important for spermosphere communities. Overall, this study advances knowledge in the assembly of the plant microbiome early in a plant's life, which may have plant health implications in more mature plant growth stages. IMPORTANCE The central hypothesis of this research was that plant species and seed exudate release would alter the assembly of microbes in the spermosphere soil. Our research investigated the response of microbes to the initial burst of nutrients into the spermosphere soil, filling knowledge gaps from previous studies that pregerminated seeds under sterile conditions. We identified several copiotrophic bacterial lineages with a long history of plant growth promotion proliferating in response to the initial exudate release. With a comparative network approach, we show that these copiotrophic bacteria are not central to networks, demonstrating that other microbes (including fungi) may be important for community structure. This study improves knowledge on microbial dynamics in the understudied spermosphere and helps inform solutions for biologically or ecologically motivated solutions to spermosphere pathogens.

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.

Bioinduced precipitation of smectites and carbonates in photosynthetic diatom-rich microbial mats: Effect of culture medium

The association of MgII clays with dolomite is common in ancient and modern lacustrine environments, although, the role of microbial activity in their precipitation remains a challenge. In this study, microbial culture experiments provide the first evidence of saponite and dolomite precipitation on diatom-bearing photosynthetic microbial mats. Microbial strains were isolated from photosynthetic microbial mats collected from Caballo Alba lake in Segovia, Spain. The microbial communities´ growth and mineral precipitates varied function of the type of media used, semi-solid or liquid, respectively. The prokaryotic composition identified from cultures was dominated by Cyanobacteria and Proteobacteria. Bacteroidetes were the most abundant heterotrophic bacteria. Saponite, aragonite, and dolomite crystals were closely attached to the phytoplanktonic communities grown in liquid cultures. Diatoms are replaced by saponite and dolomite in liquid cultures where diatoms are unprovided of protection of extracellular polymeric substances (EPS). Saponite grew around the diatom frustules, as dissolution of the biogenic silica occurs in a medium depleted in silica, replacing diatoms by saponite pseudomorphs. To a lesser extent, cyanobacterial cell walls were also covered by saponite crystals. In addition, amorphous silica of the frustules also provided a suitable template for the nucleation of dolomite crystals. Alternatively, MgII-rich aragonite crystals with fibrous morphologies precipitated within saponite crystal aggregates, suggesting that clay minerals enhanced the nucleation and precipitation of dolomite. In the semi-solid medium, where calcite precipitated in association with Cyanobacteria, diatoms were capable of developing a sheet of EPS which protected their frustules from dissolution. Here, we suggest that, in alkaline lakes phytoplanktonic diatoms might have contributed to the precipitation of clay minerals and carbonates since the Jurassic.