Prokaryotic Communities Research Articles

Sponges and their prokaryotic communities sampled from a remote karst ecosystem

Marine karst ecosystems exist at the land-sea interface and are characterised by underwater formations sculpted over time by the action of seawater. Submerged caves and crevices of these ecosystems host a rich array of marine life of which sponges are among the most abundant and diverse components. In the present study, we describe elements of the sponge fauna sampled from a unique karst ecosystem at a remote island, Orchid Island, off the southeastern coast of Taiwan. The present study includes several understudied sponge taxa, including sclerosponges (Acanthochaetetes wellsi, and Astrosclera willeyana) and several lithistid species from dark, shallow-water caves. Prokaryotic communities were obtained from a total of 22 demosponge species, of which 11 are potentially new to science. The tetracladinid, lithistids harboured prokaryotic communities, which clustered separately from all other sponge species, contrasting with the non-tetracladinid, lithistid Vetulina incrustans. The tetracladinid, lithistids, furthermore, formed two distinct clusters with species of the Spirophorina suborder clustering apart from those of the Astrophorina suborder. The sclerosponge A. wellsi also harboured a distinct prokaryotic community in terms of composition including five unique, abundant OTUs with relatively low sequence similarities to organisms in GenBank. All cave sponges were enriched with SAR202 members, a group of bacteria known for their role in the degradation of recalcitrant compounds. The highest relative abundance of SAR202 was found in A. wellsi. We propose that the cave sponges of Orchid Island may play an as-yet uncharted role in nutrient dynamics at the land-sea interface.

Impact of stockpile depth and storage time on soil microbial communities

Soil removal and stockpiling prior to mining activities have adverse effects on soil health, which raises concerns about the suitability of stockpiled soils as a reclamation substrate. Due to the fundamental roles microbes play in ecosystem function and services, they can be used as indicators of soil health and quality. We analyzed the prokaryotic microbial communities in a chronosequence of 0.5–28-year-old stockpiles at increasing depths (0–300 cm), in two oil-extraction locations in northern Alberta. Our results indicate that the microbial communities of the seven stockpiles examined were more similar to each other than to the undisturbed soils used as reference, which might indicate that stockpiling shifts the microbial community composition outside the range of natural variability. Furthermore, while microbial communities in younger and older stockpiles were dissimilar to the reference soils, the communities of intermediate-age stockpiles were more similar to those in the reference soils. We interpret these divergences in similarity to indicate that initial disturbance leads to a shift in the microbial community, which then recovers following several years of storage, but eventually, long-term storage leads to a secondary divergence from the range of natural variability. Additionally, the bacterial diversity decreased significantly with increasing stockpile depth, which could be attributed to the harsh conditions of the deeper stockpile layers and the scarcity of nutrients. Our findings provide important insights into the impact of soil stockpiling on microbial communities and complement those of earlier studies highlighting the importance of stockpile depth and storage time as predictors of variability of soil microbial diversity and community composition. Furthermore, due to the crucial functions played by microbes in soils, our conclusions should serve for reclamation agencies to modify the stockpiling protocols in order to mitigate the impact of stockpiling on soil microbial communities.

Differentiation of prokaryotic community composition in suspended sediment size-fractionation in a small loess watershed

The transfer of particle-bound prokaryotes and substrates from slopes to rivers during soil erosion is a crucial dynamic process that greatly influences terrestrial biological and geochemical cycles. Particle size strongly affects the transport distance of suspended sediments and likely induces prokaryote and substrate variations along the course of the river. Previous studies have mainly focused on the spatial redistribution of soil prokaryotes, whereas the variation in prokaryotic diversity and community composition among different particle size-fractions in suspended sediments remain unclear. In this study, suspended sediments were collected at four plots (upstream, middle stream, downstream, and dam) along a river that runs through a valley. Sampled sediments were size-fractionated into > 63 μm and < 63 μm particles (referred to as small and large particle fractions hereafter), to identify the corresponding prokaryotic community composition, interactions, and functions. The richness index (Chao1 and observed species) and the diversity index (Shannon) of sediment-associated prokaryotic communities significantly decreased from upstream towards dam plots, except in the small particle fraction in downstream and dam plots. The highest β-diversity index value was found for the large particle fractions, while the geospatial contribution to β-diversity varied. The concentration of Proteobacteria in downstream (41.39 %) and dam (34.86 %) plots was lower than that in the upstream (47.65 %) and middle stream (45.90 %) plots. In contrast, Cyanobacteria (4.89 % and 6.75 %) and Verrucomicrobiota (5.98 % and 11.00 %) concentrations were greater in the downstream and dam plots, respectively, than those in the upstream (0.93 % and 2.43 %) and middle stream (3.37 % and 3.11 %) plots, respectively. Additionally, the concentrations of Verrucomicrobiota and Bacteroidota were significantly higher in the small particle fractions (2.26–8.12 % and 4.33–7.72 %) than those in the large particle fractions (2.03–5.94 % and 3.70–7.11 %). Compared to the other plots, upstream plots had a larger clustered network and a greater number of co-occurrences within the prokaryotic community in the bulk sediment and in the small particle fraction, whereas more complex interactions among prokaryotic communities were found in the large particle fraction from the dam plots. Soil organic carbon (SOC), total nitrogen (TN), and Olsen phosphorus were the three most influential factors, explaining 67.41 % of the variation in prokaryotic community. Proteobacteria and Myxococcota correlated negatively with SOC, TN, and Olsen P but positively with C = O. Conversely, Cyanobacteria and Verrucomicrobiota correlated positively with SOC, TN, and Olsen P but negatively with C = O. Functional groups linked to the biogeochemical cycling of carbon (methanol oxidation and methylotrophy) were found in high concentrations, whereas those linked to nitrogen (nitrogen and nitrate respiration) were found in low concentrations in upstream and middle stream plots. Reassembly of the sediment physicochemical characteristics among geospatial plots along the transport transect significantly altered the prokaryotic community composition and metabolic functional groups.

Virus-prokaryote infection pairs associated with prokaryotic production in a freshwater lake.

Viruses infect and kill prokaryotic populations in a density- or frequency-dependent manner and affect carbon cycling. However, the effects of the stratification transition, including the stratified and de-stratified periods, on the changes in prokaryotic and viral communities and their interactions remain unclear. We conducted a monthly survey of the surface and deep layers of a large and deep freshwater lake (Lake Biwa, Japan) for a year and analyzed the prokaryotic production and prokaryotic and viral community composition. Our analysis revealed that, in the surface layer, 19 prokaryotic species, accounting for approximately 40% of the total prokaryotic abundance, could potentially contribute to the majority of prokaryotic production, which is the highest during the summer and is suppressed by viruses. This suggests that a small fraction of prokaryotes and phages were the key infection pairs during the peak period of prokaryotic activity in the freshwater lake. We also found that approximately 50% of the dominant prokaryotic and viral species in the deep layer were present throughout the study period. This suggests that the "kill the winner" model could explain the viral impact on prokaryotes in the surface layer, but other dynamics may be at play in the deep layer. Furthermore, we found that annual vertical mixing could result in a similar rate of community change between the surface and deep layers. These findings may be valuable in understanding how communities and the interaction among them change when freshwater lake stratification is affected by global warming in the future.IMPORTANCEViral infection associated with prokaryotic production occurs in a density- or frequency-dependent manner and regulates the prokaryotic community. Stratification transition and annual vertical mixing in freshwater lakes are known to affect the prokaryotic community and the interaction between prokaryotes and viruses. By pairing measurements of virome analysis and prokaryotic production of a 1-year survey of the depths of surface and deep layers, we revealed (i) the prokaryotic infection pairs associated with prokaryotic production and (ii) the reset in prokaryotic and viral communities through annual vertical mixing in a freshwater lake. Our results provide a basis for future work into changes in stratification that may impact the biogeochemical cycling in freshwater lakes.

Community structure and association network of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

The Bering-Chukchi shelf is one of the world's most productive areas and characterized by high benthic biomass. Sedimentary microbial communities play a crucial role in the remineralization of organic matter and associated biogeochemical cycles, reflecting both short-term changes in the environment and more consistent long-term environmental characteristics in a given habitat. In order to get a better understanding of the community structure of sediment-associated prokaryotes, surface sediments were collected from 26 stations in the Bering-Chukchi shelf and adjacent northern deep seas in this study. Prokaryote community structures were analyzed by metabarcoding of the 16S rRNA gene, and potential interactions among prokaryotic groups were analyzed by co-occurrence networks. Relationships between the prokaryote community and environmental factors were assessed. Gammaproteobacteria, Alphaproteobacteria, and Flavobacteriia were the dominant bacterial classes, contributing 35.0, 18.9, and 17.3% of the bacterial reads, respectively. The phototrophic cyanobacteria accounted for 2.7% of the DNA reads and occurred more abundantly in the Bering-Chukchi shelf. Prokaryotic community assemblages were different in the northern deep seas compared to the Bering-Chukchi shelf, represented by the lowered diversity and the increased abundant operational Taxonomic Units (OTU), suggesting that the abundant taxa may play more important roles in the northern deep seas. Correlation analysis showed that latitude, water depth, and nutrients were important factors affecting the prokaryote community structure. Abundant OTUs were distributed widely in the study area. The complex association networks indicated a stable microbial community structure in the study area. The high positive interactions (81.8-97.7%) in this study suggested that symbiotic and/or cooperative relationships accounted for a dominant proportion of the microbial networks. However, the dominant taxa were generally located at the edge of the co-occurrence networks rather than in the major modules. Most of the keystone OTUs were intermediately abundant OTUs with relative reads between 0.01 and 1%, suggesting that taxa with moderate biomass might have considerable impacts on the structure and function of the microbial community. This study enriched the understanding of prokaryotic community in surface sediments from the Bering-Chukchi shelf and adjacent sea areas.

Structural Shifts in the Soil Prokaryotic Communities Marking the Podzol-Forming Process on Sand Dumps

This work describes the microbial community structure of the continuously revegetated chronosequence of a former sand quarry, which demonstrates a unique example of nearly complete soil restoration in less than 100 years. Samples were collected at five time points (0, 3, 30, 70 years and mature soil) from the entire set of soil horizons, revealing the history of pedogenesis. Real-time PCR was applied to quantitatively describe the bacterial and archaeal communities. High-throughput sequencing of the bacterial and archaeal V4 variable region of the 16S rRNA gene was used to identify abundant microbial taxa. A beta-diversity analysis revealed that the prokaryotic community structure responded strongly to the processes of organic matter accumulation and the corresponding evolution of the soil into discrete horizons. Changes in soil microbiota in the course of soil profile evolution revealed three groups of prokaryotes, which tended to accumulate in the specific soil horizons and might be associated with the certain soil-forming processes, including plant roots growth. This research showed the heuristic potential of soil horizon profiling in microbiological studies as opposed to the formal depth-dependent separation of the soil layers. The results allowed us to trace the relationship between the structure of the soil prokaryotic community and the peculiarities of the evolution of the podzolic soil profile as well as to identify the microbial indicators and drivers of primary pedogenesis.

The Trade-Off between Enteric and Manure Methane Emissions and Their Bacterial Ecology in Lactating Cows Fed Diets Varying in Forage-to-Concentrate Ratio and Rapeseed Oil

An experiment was conducted to examine how dietary interventions reducing enteric methane (CH4) emissions influence manure CH4 emissions in biogas production (as biochemical methane potential (BMP)) or under static conditions mimicking natural manure storage conditions. Experimental treatments consisted of a factorial arrangement of high (HF: 0.65) or low (LF: 0.35) levels of forage and 0 or 50 g of rapeseed oil per kg of diet dry matter. Oil supplementation reduced daily enteric CH4 emissions, especially in the HF diet, by 20%. Greater dietary concentrate proportion reduced CH4 yield and intensity (6 and 12%, respectively) and decreased pH, increased total volatile fatty acids, and molar proportions of butyrate and valerate in feces incubated under static conditions. Oil supplementation increased daily BMP and BMP calculated per unit of organic matter (OM) (17 and 15%, respectively). Increased dietary concentrate had no impact on daily BMP and BMP per unit of OM, whereas it reduced daily CH4 production by 89% and CH4 per unit of OM by 91% under static conditions. Dietary oil supplementation tended to decrease fecal CH4 production per unit of digestible OM (23%) under static conditions. Diets had no impact on the alpha diversity of ruminal prokaryotes. After incubation, the fecal prokaryote community was significantly less diverse. Diets had no effect on alpha diversity in the BMP experiment, but static trial fecal samples originating from the HF diet showed significantly lower diversity compared with the LF diet. Overall, the tested dietary interventions reduced enteric CH4 emissions and reduced or tended to reduce manure CH4 emissions under static conditions, indicating a lack of trade-off between enteric and manure CH4 emissions. The potential for increasing CH4 yields in biogas industries due to dietary interventions could lead to a sustainable synergy between farms and industry.

Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary

Abstract Anthropogenic influences have drastically increased nutrient concentrations in many estuaries globally, and microbial communities have adapted to the resulting hypereutrophic ecosystems. However, our knowledge of the dominant microbial taxa and their potential functions in these ecosystems has remained sparse. Here, we study prokaryotic community dynamics in a temporal–spatial dataset, from a subtropical hypereutrophic estuary. Screening 54 water samples across brackish to marine sites revealed that nutrient concentrations and salinity best explained spatial community variations, whereas temperature and dissolved oxygen likely drive seasonal shifts. By combining short and long read sequencing data, we recovered 2,459 metagenome-assembled genomes, proposed new taxon names for previously uncharacterised lineages, and created an extensive, habitat specific genome reference database. Community profiling based on this genome reference database revealed a diverse prokaryotic community comprising 61 bacterial and 18 archaeal phyla, and resulted in an improved taxonomic resolution at lower ranks down to genus level. We found that the vast majority (61 out of 73) of abundant genera (&amp;gt;1% average) represented unnamed and novel lineages, and that all genera could be clearly separated into brackish and marine ecotypes with inferred habitat specific functions. Applying supervised machine learning and metabolic reconstruction, we identified several microbial indicator taxa responding directly or indirectly to elevated nitrate and total phosphorus concentrations. In conclusion, our analysis highlights the importance of improved taxonomic resolution, sheds light on the role of previously uncharacterised lineages in estuarine nutrient cycling, and identifies microbial indicators for nutrient levels crucial in estuary health assessments.

Biotic interactions explain seasonal dynamics of the alpine soil microbiome.

While it is acknowledged that alpine soil bacterial communities are primarily driven by season and elevation, there is no consensus on the factors influencing fungi and protists. Here we used a holistic approach of the microbiome to investigate the seasonal dynamics in alpine grasslands, focusing on soil food web interactions. We collected 158 soil samples along elevation transects from three mountains in the Alps, in spring during snowmelt and in the following summer. Using metatranscriptomics, we simultaneously assessed prokaryotic and eukaryotic communities, further classified into trophic guilds. Our findings reveal that the consumers' pressure increases from spring to summer, leading to more diverse and evenly distributed prey communities. Consequently, consumers effectively maintain the diverse soil bacterial and fungal communities essential for ecosystem functioning. Our research highlights the significance of biotic interactions in understanding the distribution and dynamics of alpine microbial communities.

Enrichment of putative plant growth promoting microorganisms in biodynamic compared with organic agriculture soils

Abstract The potential of soils to maintain biological productivity, defined as soil health, is strongly influenced by human activity, such as agriculture. Therefore, soil management has always been a concern for sustainable agriculture and new methods that account for both soil health and crop yield must be found. Biofertilization using microbial inoculants emerges as a promising alternative to conventional interventions such as excessive mineral fertilization and herbicide use. Biodynamic preparations used as a central part of biodynamic agriculture have various effects on soil properties, such as microbial biomass and respiration. We conducted several biomarker experiments to infer the effect of biodynamic preparations on soil prokaryotic and fungal communities and compared results to organic management. Potential plant growth promoting amplicon sequence variants were quantified using a commercial database based on their taxonomic identity. We found significantly higher numbers of putative plant growth promoting amplicon sequence variants in biodynamically compared with organically treated soils. Furthermore, prokaryotic amplicon sequence variants enriched in biodynamic preparations were found in higher numbers in biodynamically treated soils, indicating successful colonization after treatment. Experiments were conducted at three locations in Germany and 21 locations in France covering different crops and soil types. Altogether, our results indicate that biodynamic preparations can act as biofertilizers that promote soil health by increasing the abundance of plant growth promoting microorganisms.

The active free-living bathypelagic microbiome is largely dominated by rare surface taxa.

A persistent microbial seed bank is postulated to sustain the marine biosphere, and recent findings show that prokaryotic taxa present in the ocean's surface dominate prokaryotic communities throughout the water column. Yet, environmental conditions exert a tight control on the activity of prokaryotes, and drastic changes in these conditions are known to occur from the surface to deep waters. The simultaneous characterization of the total (DNA) and active (i.e. with potential for protein synthesis, RNA) free-living communities in 13 stations distributed across the tropical and subtropical global ocean allowed us to assess their change in structure and diversity along the water column. We observed that active communities were surprisingly more similar along the vertical gradient than total communities. Looking at the vertical connectivity of the active vs. the total communities, we found that taxa detected in the surface sometimes accounted for more than 75% of the active microbiome of bathypelagic waters (50% on average). These active taxa were generally rare in the surface, representing a small fraction of all the surface taxa. Our findings show that the drastic vertical change in environmental conditions leads to the inactivation and disappearance of a large proportion of surface taxa, but some surface-rare taxa remain active (or with potential for protein synthesis) and dominate the bathypelagic active microbiome.

Soil microbial community response to ectomycorrhizal dominance in diverse neotropical montane forests

Ectomycorrhizal (EM) associations can promote the dominance of tree species in otherwise diverse tropical forests. These EM associations between trees and their fungal mutualists have important consequences for soil organic matter cycling, yet the influence of these EM-associated effects on surrounding microbial communities is not well known, particularly in neotropical forests. We examined fungal and prokaryotic community composition in surface soil samples from mixed arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) stands as well as stands dominated by EM-associated Oreomunnea mexicana (Juglandaceae) in four watersheds differing in soil fertility in the Fortuna Forest Reserve, Panama. We hypothesized that EM-dominated stands would support distinct microbial community assemblages relative to the mixed AM-EM stands due to differences in carbon and nitrogen cycling associated with the dominance of EM trees. We expected that this microbiome selection in EM-dominated stands would lead to lower overall microbial community diversity and turnover, with tighter correspondence between general fungal and prokaryotic communities. We measured fungal and prokaryotic community composition via high-throughput Illumina sequencing of the ITS2 (fungi) and 16S rRNA (prokaryotic) gene regions. We analyzed differences in alpha and beta diversity between forest stands associated with different mycorrhizal types, as well as the relative abundance of fungal functional groups and various microbial taxa. We found that fungal and prokaryotic community composition differed based on stand mycorrhizal type. There was lower prokaryotic diversity and lower relative abundance of fungal saprotrophs and pathogens in EM-dominated than AM-EM mixed stands. However, contrary to our prediction, there was lower homogeneity for fungal communities in EM-dominated stands compared to mixed AM-EM stands. Overall, we demonstrate that EM-dominated tropical forest stands have distinct soil microbiomes relative to surrounding diverse forests, suggesting that EM fungi may filter microbial functional groups in ways that could potentially influence plant performance or ecosystem function.

Microbial community composition of terrestrial habitats in East Antarctica with a focus on microphototrophs.

The Antarctic terrestrial environment harbors a diverse community of microorganisms, which have adapted to the extreme conditions. The aim of this study was to describe the composition of microbial communities in a diverse range of terrestrial environments (various biocrusts and soils, sands from ephemeral wetlands, biofilms, endolithic and hypolithic communities) in East Antarctica using both molecular and morphological approaches. Amplicon sequencing of the 16S rRNA gene revealed the dominance of Chloroflexi, Cyanobacteria and Firmicutes, while sequencing of the 18S rRNA gene showed the prevalence of Alveolata, Chloroplastida, Metazoa, and Rhizaria. This study also provided a comprehensive assessment of the microphototrophic community revealing a diversity of cyanobacteria and eukaryotic microalgae in various Antarctic terrestrial samples. Filamentous cyanobacteria belonging to the orders Oscillatoriales and Pseudanabaenales dominated prokaryotic community, while members of Trebouxiophyceae were the most abundant representatives of eukaryotes. In addition, the co-occurrence analysis showed a prevalence of positive correlations with bacterial taxa frequently co-occurring together.

Nutrient-dependent cross-kingdom interactions in the hyphosphere of an arbuscular mycorrhizal fungus.

The hyphosphere of arbuscular mycorrhizal (AM) fungi is teeming with microbial life. Yet, the influence of nutrient availability or nutrient forms on the hyphosphere microbiomes is still poorly understood. Here, we examined how the microbial community (prokaryotic, fungal, protistan) was affected by the presence of the AM fungus Rhizophagus irregularis in the rhizosphere and the root-free zone, and how different nitrogen (N) and phosphorus (P) supplements into the root-free compartment influenced the communities. The presence of AM fungus greatly affected microbial communities both in the rhizosphere and the root-free zone, with prokaryotic communities being affected the most. Protists were the only group of microbes whose richness and diversity were significantly reduced by the presence of the AM fungus. Our results showed that the type of nutrients AM fungi encounter in localized patches modulate the structure of hyphosphere microbial communities. In contrast we did not observe any effects of the AM fungus on (non-mycorrhizal) fungal community composition. Compared to the non-mycorrhizal control, the root-free zone with the AM fungus (i.e., the AM fungal hyphosphere) was enriched with Alphaproteobacteria, some micropredatory and copiotroph bacterial taxa (e.g., Xanthomonadaceae and Bacteroidota), and the poorly characterized and not yet cultured Acidobacteriota subgroup GP17, especially when phytate was added. Ammonia-oxidizing Nitrosomonas and nitrite-oxidizing Nitrospira were significantly suppressed in the presence of the AM fungus in the root-free compartment, especially upon addition of inorganic N. Co-occurrence network analyses revealed that microbial communities in the root-free compartment were complex and interconnected with more keystone species when AM fungus was present, especially when the root-free compartment was amended with phytate. Our study showed that the form of nutrients is an important driver of prokaryotic and eukaryotic community assembly in the AM fungal hyphosphere, despite the assumed presence of a stable and specific AM fungal hyphoplane microbiome. Predictable responses of specific microbial taxa will open the possibility of using them as co-inoculants with AM fungi, e.g., to improve crop performance.

Coastal upwelling systems as dynamic mosaics of bacterioplankton functional specialization

Coastal upwelling areas are extraordinarily productive environments where prokaryotic communities, the principal remineralizers of dissolved organic matter (DOM), rapidly respond to phytoplankton bloom and decay dynamics. Nevertheless, the extent of variability of key microbial functions in such dynamic waters remains largely unconstrained. Our metatranscriptomics analyses of 162 marker genes encoding ecologically relevant prokaryotic functions showed distinct spatial-temporal patterns in the NW Iberian Peninsula upwelling area. Short-term (daily) changes in specific bacterial functions associated with changes in biotic and abiotic factors were superimposed on seasonal variability. Taxonomic and functional specialization of prokaryotic communities, based mostly on different resource acquisition strategies, was observed. Our results uncovered the potential influence of prokaryotic functioning on phytoplankton bloom composition and development (e.g., Cellvibrionales and Flavobacteriales increased relative gene expression related to vitamin B12 and siderophore metabolisms during Chaetoceros and Dinophyceae summer blooms). Notably, bacterial adjustments to C- or N-limitation and DMSP availability during summer phytoplankton blooms and different spatial-temporal patterns of variability in the expression of genes with different phosphate affinity indicated a complex role of resource availability in structuring bacterial communities in this upwelling system. Also, a crucial role of Cellvibrionales in the degradation of DOM (carbohydrate metabolism, TCA cycle, proteorhodopsin, ammonium, and phosphate uptake genes) during the summer phytoplankton bloom was found. Overall, this dataset revealed an intertwined mosaic of microbial interactions and nutrient utilization patterns along a spatial-temporal gradient that needs to be considered if we aim to understand the biogeochemical processes in some of the most productive ecosystems in the world´s oceans.

Changes in the Microbial Community Associated with the Large Benthic Foraminifera Cycloclypeus Carpenteri, Along a Depth Gradient

Abstract Cycloclypeus carpenteri is one of the deepest living large benthic foraminifera. It has an obligatory relationship with diatom photosymbionts, and, in addition, houses a diverse prokaryotic community. Variations in the eukaryotic and prokaryotic endobiotic community composition might be key in allowing Cycloclypeus to occur in low light environments. We assessed the variability of the prokaryotic and eukaryotic communities associated with Cycloclypeus along a depth gradient from 50 to 130 m at two locations in the Federated States of Micronesia (Northwest Pacific) by metabarcoding of the 18S V9 rRNA region for eukaryotes and the 16S V3-V4 rRNA region for prokaryotes. We observed a single foraminiferal operational taxonomic unit (OTU), as well as a single dominant diatom OTU that was abundant in all sequenced specimens. Both the prokaryotic and the eukaryotic endobiotic communities (excluding the dominant diatom) changed with water depth and associated irradiance levels. We observed a distinct change in the prokaryotic community composition around 90–100 m water depth at Pohnpei, equivalent to ∼1% surface radiation. This change in microbial communities in the Cycloclypeus holobiont suggests a potential role of the associated microbial communities in accommodating differences in (micro)habitat, although we cannot exclude that the prokaryote community is to a large extent driven by their community composition in the ambient environment.

Prokaryote communities along a source-to-estuary river continuum in the Brazilian Atlantic Forest.

The activities of microbiomes in river sediments play an important role in sustaining ecosystem functions by driving many biogeochemical cycles. However, river ecosystems are frequently affected by anthropogenic activities, which may lead to microbial biodiversity loss and/or changes in ecosystem functions and related services. While parts of the Atlantic Forest biome stretching along much of the eastern coast of South America are protected by governmental conservation efforts, an estimated 89% of these areas in Brazil are under threat. This adds urgency to the characterization of prokaryotic communities in this vast and highly diverse biome. Here, we present prokaryotic sediment communities in the tropical Juliana River system at three sites, an upstream site near the river source in the mountains (Source) to a site in the middle reaches (Valley) and an estuarine site near the urban center of Ituberá (Mangrove). The diversity and composition of the communities were compared at these sites, along with environmental conditions, the former by using qualitative and quantitative analyses of 16S rRNA gene amplicons. While the communities included distinct populations at each site, a suite of core taxa accounted for the majority of the populations at all sites. Prokaryote diversity was highest in the sediments of the Mangrove site and lowest at the Valley site. The highest number of genera exclusive to a given site was found at the Source site, followed by the Mangrove site, which contained some archaeal genera not present at the freshwater sites. Copper (Cu) concentrations were related to differences in communities among sites, but none of the other environmental factors we determined was found to have a significant influence. This may be partly due to an urban imprint on the Mangrove site by providing organic carbon and nutrients via domestic effluents.

Prokaryotic Community Composition and Diversity in Sediments from Choctafaula, Uphapee, and Cubahatchee Creeks in the Lower Tallapoosa River Basin, Macon County, Alabama: An Observational Study

Sedimentary prokaryotes are primarily responsible for metabolic activity in rivers. They are subjected to a variety of natural and anthropogenic pressures, allowing us to use the composition and diversity of their communities as indicators of ecological health. For our investigation, we looked at sediments from three ecologically critical streams in the Lower Tallapoosa River Basin (Choctafaula, Uphapee, and Cubahatchee Creeks). The prokaryotic community was characterized using molecular approaches, and elemental concentrations were determined by inductively coupled plasma atomic emission spectrometry. This research demonstrated that Proteobacteria (45.02–80.73%), Bacteroidetes (1.98–26.52%), Firmicutes (1.36–50.67%), Actinobacteria (1.55–16.81%), and Acidobacteria (0.13–8.77%) were the most prevalent phyla. Key physicochemical parameters, core communities at multiple taxonomic levels, and several pathogenic genera shifted radically between streams. Weighted and unweighted unifrac distance metrics based PCoA plots indicated the structural and membership similarity of samples from specific creek ecosystems. Based on our research findings, it is evident that the composition and diversity of prokaryotic communities in sediment could serve as significant indicators in stream ecosystems. Further investigation and application of these indicators could prove valuable in assessing the health of streams, particularly in light of the accelerated changes resulting from climate change within a condensed timeframe.

Global citrus root microbiota unravels assembly cues and core members.

Citrus is one of the most important fruit crops worldwide, and the root-associated microbiota can have a profound impact on tree health and growth. In a collaborative effort, the International Citrus Microbiome Consortium investigated the global citrus root microbiota with samples collected from nine citrus-producing countries across six continents. We analyzed 16S rDNA and ITS2 amplicon sequencing data to identify predominant prokaryotic and fungal taxa in citrus root samples. Comparative analyses were conducted between root-associated microbial communities and those from the corresponding rhizosphere and bulk soil samples. Additionally, genotype-based group-wise comparisons were performed to assess the impact of citrus genotype on root microbiota composition. Ten predominant prokaryotic phyla, containing nine bacterial phyla including Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroidetes and one archaeal phylum (Thaumarchaeota), and multiple fungal phyla including Ascomycota and Basidiomycota were identified in the citrus root samples. Compared with the microbial communities from the corresponding rhizosphere and bulk soil samples from the same trees, the prokaryotic and fungal communities in the roots exhibited lower diversity and complexity but greater modularity compared to those in the rhizosphere. In total, 30 root-enriched and 150 root-depleted genera in bacterial community were identified, whereas 21 fungal genera were enriched, and 147 fungal genera were depleted in the root niche compared with the rhizosphere. The citrus genotype significantly affected the root prokaryotic and fungal communities. In addition, we have identified the core root prokaryotic genera comprising Acidibacter, Allorhizobium, Bradyrhizobium, Chitinophaga, Cupriavidus, Devosia, Dongia, Niastella, Pseudomonas, Sphingobium, Steroidobacter and Streptomyces, and the core fungal genera including Acrocalymma, Cladosporium, Fusarium, Gibberella, Mortierella, Neocosmospora and Volutella. The potential functions of these core genera of root microbiota were predicted. Overall, this study provides new insights into the assembly of microbial communities and identifies core members of citrus root microbiota across a wide geographic range. The findings offer valuable information for manipulating root microbiota to enhance plant growth and health.

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.