Prokaryotic Communities Research Articles

‘Altruistic’ cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics

Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5–22 % [w/v]) were Methanobacteriota (formerly “Euryarchaeota”), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36–39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.

Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments

The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.

Novel metagenomics analysis of stony coral tissue loss disease.

Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and affected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available metagenomic sequencing samples of SCTLD lesions and healthy tissues from 4 stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. These reads were then used as a reference to which we matched and removed reads from diseased lesion tissue samples, and the remaining reads associated only with disease lesions were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. To assess the utility of our pipeline, a species-level analysis of a candidate genus, Vibrio, was used to demonstrate the pipeline's effectiveness. Our approach revealed both complementary and unique coral microbiome members compared with a prior metagenome analysis of the same dataset.

Characterization of Prokaryotic Community Dynamics and Functional Profiles in Soils Contaminated Long Term with Petroleum Hydrocarbons in Response to the Addition of Soil Bioremediation Nutrients

Characterization of Prokaryotic Community Dynamics and Functional Profiles in Soils Contaminated Long Term with Petroleum Hydrocarbons in Response to the Addition of Soil Bioremediation Nutrients

Seasonal changes in soil biofilm microbial communities

Biofilm and planktonic prokaryotic communities were studied using a glass fibre filter as trapping material immersed in field soil at different times of the year (January, April, July, September) and incubated there for different periods (3, 6, 9, 12 months). The composition of biofilm and planktonic communities fluctuated over time, likely shaped by succession processes and varying environmental factors. This highlights soil biofilms as dynamic structures whose microbial community differs from that of soil plankton. Additionally, quantification of the biofilm-to-plankton 16S rRNA gene copy number ratio indicated that soil prokaryotes occur mainly as biofilm components.

Handwashing basins and healthcare associated infections: Bacterial diversity in biofilms on faucets and drains

BackgroundIncreasingly, hospital handwashing basins have been identified as a source of healthcare-associated infections. Biofilms formed on the faucet and drains of handbasins can potentially harbour pathogenic microbes and promote the dissemination of antimicrobial resistance. However, little is known about the diversity of these biofilm communities and the routes of contamination. AimThe aim of this paper was to use 16S rRNA gene amplicon sequencing to investigate the diversity of prokaryote communities present in faucet and drain biofilm samples taken from hospital and residential handbasins. FindingsThe biofilm prokaryotes communities were diverse, with high abundances of potentially corrosive, biofilm forming and pathogenic genera, including those that are not typically waterborne. The β-diversity showed statistically significant differences in the variation of bacterial communities on the basis on building type (hospital vs residential p = 0.0415). However, there was no statistically significant clustering based on sampling site (faucet vs drain p = 0.46). When examining the β-diversity between individual factors, there was a significant difference between drain biofilms of different buildings (hospital drain vs residential drain p = 0.0338). ConclusionThis study demonstrated that biofilms from hospital and residential handbasins contain complex and diverse microbial communities that differ significantly by building type. It also showed biofilms formed on the faucet and drain of a hospital's handbasins were not significantly different. Future research is needed to understand the potential mechanisms of transfer between drains and faucets of hospital handbasins. This information will inform improved infection control guidelines to control this underrecognized source of infections.

Seasonal and interannual variability of the free-living and particle-associated bacteria of a coastal microbiome.

Marine microbial communities differ genetically, metabolically, and ecologically according to their lifestyle, and they may respond differently to environmental changes. In this study, we investigated the seasonal dynamics of bacterial assemblies in the free-living (FL) and particle-associated (PA) fractions across a span of 6 years in the Blanes Bay Microbial Observatory in the Northwestern Mediterranean. Both lifestyles showed marked seasonality. The trends in alpha diversity were similar, with lower values in spring-summer than in autumn-winter. Samples from both fractions were grouped seasonally and the percentage of community variability explained by the measured environmental variables was comparable (32% in FL and 31% in PA). Canonical analyses showed that biotic interactions were determinants of bacterioplankton dynamics and that their relevance varies depending on lifestyles. Time-decay curves confirmed a high degree of predictability in both fractions. Yet, 'seasonal' Amplicon Sequence Variants (ASVs) (as defined by Lomb Scargle time series analysis) in the PA communities represented 46% of the total relative abundance while these accounted for 30% in the FL fraction. These results demonstrate that bacteria inhabiting both fractions exhibit marked seasonality, highlighting the importance of accounting for both lifestyles to fully comprehend the dynamics of marine prokaryotic communities.

Diversity, composition and potential roles of sedimentary microbial communities in different coastal substrates around subtropical Okinawa Island, Japan

BackgroundMarine benthic prokaryotic communities play crucial roles in material recycling within coastal environments, including coral reefs. Coastal sedimentary microbiomes are particularly important as potential reservoirs of symbiotic, beneficial, and pathogenic bacteria in coral reef environments, and therefore presumably play a core role in local ecosystem functioning. However, there is a lack of studies comparing different environments with multiple sites on the island scale, particularly studies focusing on prokaryotic communities, as previous investigations have focused mainly on a single site or on specific environmental conditions. In our study, we collected coastal sediments from seven sites around Okinawa Island, Japan, including three different benthic types; sandy bottoms, seagrass meadows, and hard substratum with living scleractinian corals. We then used metabarcoding to identify prokaryotic compositions and estimate enzymes encoded by genes to infer their functions.ResultsThe results showed that the three substrata had significantly different prokaryotic compositions. Seagrass meadow sites exhibited significantly higher prokaryotic alpha-diversity compared to sandy bottom sites. ANCOM analysis revealed that multiple bacterial orders were differentially abundant within each substratum. At coral reef sites, putative disease- and thermal stress-related opportunistic bacteria such as Rhodobacterales, Verrucomicrobiales, and Cytophagales were comparatively abundant, while seagrass meadow sites abundantly harbored Desulfobacterales, Steroidobacterales and Chromatiales, which are common bacterial orders in seagrass meadows. According to our gene-coded enzyme analyses the numbers of differentially abundant enzymes were highest in coral reef sites. Notably, superoxide dismutase, an important enzyme for anti-oxidative stress in coral tissue, was abundant at coral sites. Our results provide a list of prokaryotes to look into in each substrate, and further emphasize the importance of considering the microbiome, especially when focusing on environmental conservation.ConclusionOur findings prove that prokaryotic metabarcoding is capable of capturing compositional differences and the diversity of microbial communities in three different environments. Furthermore, several taxa were suggested to be differentially more abundant in specific environments, and gene-coded enzymic compositions also showed possible differences in ecological functions. Further study, in combination with field observations and temporal sampling, is key to achieving a better understanding of the interactions between the local microbiome and the surrounding benthic community.

Strong Saharan Dust Deposition Events Alter Microbial Diversity and Composition in Sediments of High-Mountain Lakes of Sierra Nevada (Spain)

Mediterranean high-mountain lakes are being increasingly affected by strong Saharan dust deposition events. However, the ecological impacts of these severe atmospheric episodes remain largely unknown. We examined the effects of a strong Saharan dust intrusion to the Iberian Peninsula in 2022 on the physicochemical parameters and prokaryotic communities in sediments of nine high-mountain lakes of Sierra Nevada (Spain) located above 2800 m.a.s.l and in different orientations (north vs. south). A previous year (2021), with lower Saharan dust deposition with respect to 2022, was used for interannual comparisons. The strong dust deposition to the high-mountain lakes resulted in a significant increase in sediment nutrient availability which was linked to changes in the composition of prokaryotic communities. Decreases in alpha diversity and changes in beta diversity of prokaryotic communities were mainly observed in lakes located in the south compared to the north orientation likely because the former was more affected by the atmospheric dust deposition episode. Dust intrusion to the high-mountain lakes resulted in significant changes in the relative abundance of specific genera involved in important nutrient cycling processes such as phosphate solubilization, nitrogen fixation, nitrification, and denitrification. Saharan dust deposition also increased predicted microbial functionality in all lakes. Our findings show that severe atmospheric dust inputs to remote high-mountain lakes of Sierra Nevada can have significant biogeochemical and biodiversity consequences through changes in nutrient availability and prokaryotic communities in sediments of these freshwater ecosystems. This information contributes to understanding how Mediterranean high-mountain lakes of Sierra Nevada face strong intrusions of Saharan dust and their ecological consequences.

Erratum to: Prokaryotic Communities during the Self-Infestation of a Chemical Industry Waste Storage Facility

Erratum to: Prokaryotic Communities during the Self-Infestation of a Chemical Industry Waste Storage Facility

Prokaryotic and eukaryotic microbial community dynamics in biofloc systems supplemented with non-starch polysaccharides

Biofloc technology has been developed as a sustainable system in aquaculture, which uses microbial processes to remove nutrients from the water and convert them into microbial biomass. For optimal performance, the addition of carbohydrates is essential, while their type can regulate microbial activity and composition. Specifically, we hypothesize that dietary supplementation of wheat bran, containing indigestible carbohydrates such as non-starch polysaccharides, can provide complex substrates supporting diverse microbial communities within the biofloc. In this study, we investigated how higher dietary wheat bran input affected the biofloc prokaryotic and eukaryotic microbial communities in Pacific white shrimp (Litopenaeus vannamei) culture. Two pelleted diets were made: a control diet (CONdiet) with a composition similar to a commercial shrimp diet, and a diet rich in non-starch polysaccharides (WBdiet), which was created by adding wheat bran to the control diet ingredient mix, before pelleting. These two diets were fed isonitrogenous to the shrimp for 42 days, and sampling of the biofloc was performed every three weeks. The results showed shifts in both the alpha and beta diversity in biofloc during the experiment. Diet had a significant effect on the prokaryotic community composition in the biofloc at the end of the culture period, with several genera being enriched in biofloc tanks fed the WBdiet such as Muricauda, Pirellula, and Cyanobacteriaceae. Regarding the eukaryotic communities, overall, only a few taxa were significantly affected within the WBdiet, belonging to the Trebouxiophyceae and Suillus groups. Interestingly, when feeding the WBdiet, the biofloc microbial communities exhibited predicted functionalities that were more abundant in carbohydrate metabolism, and specifically related to pentose, fructose, mannose and galactose metabolism. These results provide a basis for the control of biofloc microbial communities by using ingredients rich in plant-derived non-starch polysaccharides which shrimp cannot digest but are good energy source for the microbiota in the biofloc.

The microbiome structure and shifts in surface and subsurface soil horizon of Haplic Luvisol under different crops cultivation

The presented study investigated the comparative approach to evaluate prokaryotic and fungal soil communities in association with various plant crops along the genetic soil horizon using a high-throughput sequencing technique, with special emphasis on subsoils. We evaluate the diversity, abundance and structure of soil microbiome through the depth profiles in Haplic Luvisol (Cutanic) soil collected from lucerne, pear orchard, vineyard, and wheat crop. The structure of soil microbial communities differed due to crop type as well as depth of soil layer. Additionally, some basic physicochemical properties (e.g. total organic carbon - TOC, total nitrogen - TN, dissolved organic carbon - DOC, dissolved nitrogen – DN, pH, clay content) as well as mass and morphological parameters of the plant roots were determined. The highest clay content was noted in illuvial (Bt) horizons (in all profiles). The content of the studied C and N forms was the highest in the Ap horizon and in some subsurface layers and generally decreased with depth. Generally, the highest TOC, TN and DOC content was noted in the orchard profile, while the lowest occurred in the vineyard profile. The opposite trend was found for available Mg content. In turn, the highest DN was determined in the winter wheat profile. Overall, the decrease of the abundances of the most dominant phyla with depth was observed. Using a holistic approach via microbiome investigation of bacterial and fungal communities along soil horizon in a long-term land use with different plant cultivation, we showed that land management not only affect α-diversity but also shift the structure and the composition of bacterial and fungal communities in response to land use, in particular we identified the highest values of biodiversity indicators were found under lucerne and the lowest under vineyard. Future work needs to include the importance of soil type in shaping soil microbial communities under the same land use and plant cultivation, especially under subsurface soil layers.

Manipulation of sward diversity is a more effective management strategy than addition of microbial inoculants in intensively managed grassland

Abstract Background and aims Diversifying grassland sward composition and application of microbial inoculants are potential alternative routes to facilitate enhanced nutrient acquisition by plants, but their relative effects have been rarely tested in grasslands. In a two-year field experiment, we investigated the impact of inoculants and sward types on forage yield, nutrient uptake, and the soil microbiome. Methods We implemented a fully factorial experiment with inoculants (eight levels; arbuscular mycorrhizal fungi (AMF), Paraburkholderia phytofirmans PsJN and Bacillus sp. P5 (P5), applied singly and in combination), and sward types (three levels: grass-only, grass and legume, mixture of grass, legume, and herb) as the two factors. Results In both years, there was a very strong effect of sward type, with the grass + legume and grass + legume + herb swards having much higher yields and nutrient uptake (N, P, K, S, Ca, Mg, Zn, Cu) than grass-only. Generally, there was no effect of the inoculants on yield and nutrient uptake, with limited exceptions involving AMF + P5. The best-performing microbial inoculant increased forage yield by 597 kg/ha/year, while switching from grass-only to one of the other sward types increased forage yield by 3932 kg/ha/year (grass + legume) and 4693 kg/ha/year (grass + legume + herb). The inoculants persisted in plots for > 1 year after application. Inoculants and sward type significantly affected the overall prokaryotic and fungal community structures. Conclusion Overall, under controlled field plot conditions, including legumes and herbs in a grass sward proved to be a far better farm-scale management strategy for increasing grassland forage yield and nutrient uptake than the application of microbial inoculants.

Viral and Bacterial Community Dynamics in Food Waste and Digestate from Full-Scale Biogas Plants.

Anaerobic digestion (AD) is commonly used in food waste treatment. Prokaryotic microbial communities in AD of food waste have been comprehensively studied. The role of viruses, known to affect microbial dynamics and metabolism, remains largely unexplored. This study employed metagenomic analysis and recovered 967 high-quality viral bins within food waste and digestate derived from 8 full-scale biogas plants. The diversity of viral communities was higher in digestate. In silico predictions linked 20.8% of viruses to microbial host populations, highlighting possible virus predators of key functional microbes. Lineage-specific virus-host ratio varied, indicating that viral infection dynamics might differentially affect microbial responses to the varying process parameters. Evidence for virus-mediated gene transfer was identified, emphasizing the potential role of viruses in controlling the microbiome. AD altered the specific process parameters, potentially promoting a shift in viral lifestyle from lysogenic to lytic. Viruses encoding auxiliary metabolic genes (AMGs) were involved in microbial carbon and nutrient cycling, and most AMGs were transcriptionally expressed in digestate, meaning that viruses with active functional states were likely actively involved in AD. These findings provided a comprehensive profile of viral and bacterial communities and expanded knowledge of the interactions between viruses and hosts in food waste and digestate.

Extremely halophilic brine community manipulation shows higher robustness of microbiomes inhabiting human-driven solar saltern than naturally driven lake.

Viruses greatly influence succession and diversification of their hosts, yet the effects of viral infection on the ecological dynamics of natural microbial populations remain poorly understood, especially at finer scales of diversity. By manipulating the viral predation pressure by autochthonous and allochthonous viruses, we uncovered potential phage-host interaction, and their important role in structuring the prokaryote community at an ecotype level.

Combined effects of micropollutants and their degradation on prokaryotic communities at the sediment–water interface

Pesticides and pharmaceuticals enter aquatic ecosystems as complex mixtures. Various processes govern their dissipation and effect on the sediment and surface waters. These micropollutants often show persistence and can adversely affect microorganisms even at low concentrations. We investigated the dissipation and effects on procaryotic communities of metformin (antidiabetic drug), metolachlor (agricultural herbicide), and terbutryn (herbicide in building materials). These contaminants were introduced individually or as a mixture (17.6 µM per micropollutant) into laboratory microcosms mimicking the sediment–water interface. Metformin and metolachlor completely dissipated within 70 days, whereas terbutryn persisted. Dissipation did not differ whether the micropollutants were introduced individually or as part of a mixture. Sequence analysis of 16S rRNA gene amplicons evidenced distinct responses of prokaryotic communities in both sediment and water. Prokaryotic community variations were mainly driven by matrix composition and incubation time. Micropollutant exposure played a secondary but influential role, with pronounced effects of recalcitrant metolachlor and terbutryn within the micropollutant mixture. Antagonistic and synergistic non-additive effects were identified for specific taxa across taxonomic levels in response to the micropollutant mixture. This study underscores the importance of considering the diversity of interactions between micropollutants, prokaryotic communities, and their respective environments when examining sediment–water interfaces affected by multiple contaminants.

Distributions, interactions, and dynamics of prokaryotes and phages in a hybrid biological wastewater treatment system

BackgroundUnderstanding the interactions and dynamics of microbiotas within biological wastewater treatment systems is essential for ensuring their stability and long-term sustainability. In this study, we developed a systematic framework employing multi-omics and Hi-C sequencing to extensively investigate prokaryotic and phage communities within a hybrid biofilm and activated sludge system.ResultsWe uncovered distinct distribution patterns, metabolic capabilities, and activities of functional prokaryotes through the analysis of 454 reconstructed prokaryotic genomes. Additionally, we reconstructed a phage catalog comprising 18,645 viral operational taxonomic units (vOTUs) with high length and contiguity using hybrid assembly, and a distinct distribution of phages was depicted between activated sludge (AS) and biofilm. Importantly, 1340 host-phage pairs were established using Hi-C and conventional in silico methods, unveiling the host-determined phage prevalence. The majority of predicted hosts were found to be involved in various crucial metabolic processes, highlighting the potential vital roles of phages in influencing substance metabolism within this system. Moreover, auxiliary metabolic genes (AMGs) related to various categories (e.g., carbohydrate degradation, sulfur metabolism, transporter) were predicted. Subsequent activity analysis emphasized their potential ability to mediate host metabolism during infection. We also profiled the temporal dynamics of phages and their associated hosts using 13-month time-series metagenomic data, further demonstrating their tight interactions. Notably, we observed lineage-specific infection patterns, such as potentially host abundance- or phage/host ratio-driven phage population changes.ConclusionsThe insights gained from this research contribute to the growing body of knowledge surrounding interactions and dynamics of host-phage and pave the way for further exploration and potential applications in the field of microbial ecology.7mTZubWt51_LqpKWPutADaVideo

Biogeography and dynamics of prokaryotic and microeukaryotic community assembly across 2600 km in the coastal and shelf ecosystems of the China Seas

Marine prokaryotes and microeukaryotes are essential components of microbial food webs, and drive the biogeochemical cycling. However, the underlying ecological mechanisms driving prokaryotic and microeukaryotic community assembly in large-scale coastal ecosystems remain unclear. In this study, we studied biogeographic patterns of prokaryotic and microeukaryotic communities in the coastal and shelf ecosystem of the China Seas. Results showed that prokaryotic richness was the highest in the Yangtze River Plume, whereas microeukaryotic richness decreased from south to north. Prokaryotic-microeukaryotic co-occurrence networks display greater complexity in the Yangtze River Plume compared to other regions, potentially indicating higher environmental heterogeneity. Furthermore, the cross-domain networks revealed that prokaryotes were more interconnected with each other than with microeukaryotes or between microeukaryotes, and all hub nodes were bacterial taxa, suggesting that prokaryotes may be more important for sustaining the stability and multifunctionality of coastal ecosystem than microeukaryotes. Variation Partitioning Analysis revealed that approximately equal proportions of environmental, biotic and spatial factors contribute to variations in microbial community composition. Temperature was the primary environmental driver of both prokaryotic and microeukaryotic communities across the China Seas. Additionally, stochastic processes (dispersal limitation) and deterministic processes (homogeneous selection) were two major ecological factors in shaping microeukaryotic and prokaryotic assemblages, respectively, suggesting their different environmental plasticity and evolutionary mechanisms. Overall, these results demonstrate both prokaryotic and microeukaryotic communities displayed a latitude-driven distribution pattern and different assembly mechanisms, improving our understanding of microbial biogeography patterns under global change and anthropogenic activity driven habitat diversification in the coastal and shelf ecosystem.

Consistent prokaryotic community patterns along the radial root axis of two Zea mays L. landraces across two distinct field locations.

The close interconnection of plants with rhizosphere- and root-associated microorganisms is well recognized, and high expectations are raised for considering their symbioses in the breeding of future crop varieties. However, it is unclear how consistently plant-mediated selection, a potential target in crop breeding, influences microbiome members compared to selection imposed by the agricultural environment. Landraces may have traits shaping their microbiome, which were lost during the breeding of modern varieties, but knowledge about this is scarce. We investigated prokaryotic community composition along the radial root axis of two European maize (Zea mays L.) landraces. A sampling gradient included bulk soil, a distal and proximal rhizosphere fraction, and the root compartment. Our study was replicated at two field locations with differing edaphic and climatic conditions. Further, we tested for differences between two plant developmental stages and two precipitation treatments. Community data were generated by metabarcoding of the V4 SSU rRNA region. While communities were generally distinct between field sites, the effects of landrace variety, developmental stage, and precipitation treatment were comparatively weak and not statistically significant. Under all conditions, patterns in community composition corresponded strongly to the distance to the root. Changes in α- and β-diversity, as well as abundance shifts of many taxa along this gradient, were similar for both landraces and field locations. Most affected taxa belonged to a core microbiome present in all investigated samples. Remarkably, we observed consistent enrichment of Actinobacteriota (particularly Streptomyces, Lechevalieria) and Pseudomonadota (particularly Sphingobium) toward the root. Further, we report a depletion of ammonia-oxidizers along this axis at both field sites. We identified clear enrichment and depletion patterns in microbiome composition along the radial root axis of Z. mays. Many of these were consistent across two distinct field locations, plant developmental stages, precipitation treatments, and for both landraces. This suggests a considerable influence of plant-mediated effects on the microbiome. We propose that the affected taxa have key roles in the rhizosphere and root microbiome of Z. mays. Understanding the functions of these taxa appears highly relevant for the development of methods aiming to promote microbiome services for crops.

Methane-cycling microbial communities from Amazon floodplains and upland forests respond differently to simulated climate change scenarios

Seasonal floodplains in the Amazon basin are important sources of methane (CH4), while upland forests are known for their sink capacity. Climate change effects, including shifts in rainfall patterns and rising temperatures, may alter the functionality of soil microbial communities, leading to uncertain changes in CH4 cycling dynamics. To investigate the microbial feedback under climate change scenarios, we performed a microcosm experiment using soils from two floodplains (i.e., Amazonas and Tapajós rivers) and one upland forest. We employed a two-factorial experimental design comprising flooding (with non-flooded control) and temperature (at 27 °C and 30 °C, representing a 3 °C increase) as variables. We assessed prokaryotic community dynamics over 30 days using 16S rRNA gene sequencing and qPCR. These data were integrated with chemical properties, CH4 fluxes, and isotopic values and signatures. In the floodplains, temperature changes did not significantly affect the overall microbial composition and CH4 fluxes. CH4 emissions and uptake in response to flooding and non-flooding conditions, respectively, were observed in the floodplain soils. By contrast, in the upland forest, the higher temperature caused a sink-to-source shift under flooding conditions and reduced CH4 sink capability under dry conditions. The upland soil microbial communities also changed in response to increased temperature, with a higher percentage of specialist microbes observed. Floodplains showed higher total and relative abundances of methanogenic and methanotrophic microbes compared to forest soils. Isotopic data from some flooded samples from the Amazonas river floodplain indicated CH4 oxidation metabolism. This floodplain also showed a high relative abundance of aerobic and anaerobic CH4 oxidizing Bacteria and Archaea. Taken together, our data indicate that CH4 cycle dynamics and microbial communities in Amazonian floodplain and upland forest soils may respond differently to climate change effects. We also highlight the potential role of CH4 oxidation pathways in mitigating CH4 emissions in Amazonian floodplains.