Oxygen-dependent dynamics of metformin biodegradation at the sediment-water interface and non-additive effects on prokaryotic communities.

Effects of nitrogen and phosphorus addition on microbial community composition and element cycling in a grassland soil

As a fundamental part of the soil ecosystem, prokaryotes are involved in the preservation of soil functions. However, little is known of how the combined application of long-term organic and inorganic nitrogen fertilizer affects the prokaryotic communities’ dynamics at a paddy field. A long-term positioning experiment initiated in 2013 with four treatments (NO: no N fertilizer, CN: 100% urea N with no organic fertilizer, PM: 80% urea N plus 20% N with pig manure, CM: 80% urea N plus 20% N with compost) were applied to detect the differential responses of soil physicochemical properties, and prokaryotic community structure and composition in different fertilization regimes. The results indicated that the long-term combined application of organic and inorganic nitrogen fertilizers altered the physicochemical properties to some extent and, simultaneously, established unique prokaryotic communities. In detail, the treatment of PM and CM significantly increased the content of soil organic carbon (SOC) and total nitrogen (TN) compared to NO. Moreover, a total of 31 indicator taxa were screened across the four treatments by LDA Effect Size (LEfSe) analysis following the principle of the greatest differences, which suggests that these indicator taxa were more sensitive to the fertilization. This research suggested that the combined application of long-term organic and inorganic nitrogen fertilizers not only contributed to the soil’s physicochemical properties but also changed the prokaryotic community composition.

Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P < 0.05). Variation-partitioning analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.

Altitude-dependent influence of Artemisia brevifolia on its rhizosphere microbiome in Ladakh region of the Western Himalayas

CARD-FISH analysis of prokaryotic community composition and abundance along small-scale vegetation gradients in a dry arctic tundra ecosystem

In the barren semiarid landscape individual plant species improve soil structure, reducing the erosion risks, whereby microaggregates form the most fundamental soil structural components. Extracellular polymeric substances (EPS) are considered as an important glue determining aggregation in addition to inorganic binding agents such as carbonates. However, the role of the prokaryotic community in EPS formation and consequently for microaggregation in natural environments is not substantially clarified yet. EPS should be particularly important under semiarid conditions as it forms a protection mechanisms of the prokaryotes against desiccation. Therefore, we examined the influence of the prokaryotic community on soil EPS content and subsequently on soil microaggregation in semiarid grasslands, depending on the parent material, common plant species and the distance to the plant. Soil samples were taken over a distance gradient from two major semiarid grassland plant species in Southern Spain, the legume shrub Anthyllis cytisoides and the grass tussock Macrochloa tenacissima, to the surrounding bare soil at two sites, rich and poor in carbonates. Total community DNA and EPS were extracted, followed by quantification of EPS-saccharide and bacterial abundance and examination of the prokaryotic community composition. Further, the particle size distribution of the microaggregate fraction was determined as an indication of microaggregation. We found that the overall prokaryotic community composition differed between the two sites, but not between plant species. Nonetheless, a link between the community composition and EPS content was established, whereby soil organic matter (OM) seems to be a regulating factor as increasing soil OM contents resulted in more EPS-saccharide. Furthermore, microaggregation was enhanced by the canopy, especially at the edge of Macrochloa tussocks. Contrary to the expectation that increasing inorganic C contents would diminish importance of EPS, the parent material richest in inorganic C results in a significant effect of EPS-saccharide content on microaggregation. For the inorganic C poor site, EPS-saccharide had no observed direct effect on microaggregation. Based on our results we conclude that the availability of decomposable OM influences the prokaryotic community composition and thereby triggers EPS production whereas large contents of polyvalent cations promote the stabilizing effect of EPS on microaggregates.

Agricultural activity on drained lowlands is a common practice in Denmark and there are suggestions to rewet some of them for climate mitigation purposes. Rewetting those lowlands might result in a change in microbial community composition. This study investigates the current prokaryotic diversity and community composition in soil samples from cultivated lowlands to provide the baseline for monitoring changes after rewetting. Furthermore, variations in soil properties between sites are examined, and the properties driving differences in prokaryotic diversity and community composition are identified. In total, 116 samples were collected from field sites across Denmark that were categorized as one of four different land-use types: Crop, Grass, Fallow, and Other. Soil properties were selected to cover chemical (soil water repellency, pH, electrical conductivity), hydrological (depth to ground-water table, soil water content at field capacity (-100 hPa)), nutrient-related (total nitrogen, organic carbon, carbon-to-nitrogen-ratio, fractions of pyrolizable and residual organic matter), and structural (total porosity, pore size distribution index) functions of the soil. Soil samples exhibited significant variations in their chemical and physical properties, including pH ranging from 2.02 to 7.55, organic carbon ranging from 3 g 100g-1 to 50 g 100g-1, soil water repellency ranging from 71.27 mN m-1 (hydrophilic) to 33.85 mN m-1 (very strongly hydrophobic), and total porosity ranging from 51% to 95%. Soil samples clustered according to soil class (mineral, organo-mineral, organic, highly organic) but not according to land-use type (crop, grass, fallow, other). Prokaryotic alpha diversity, measured as Shannon&amp;#8217;s diversity index (H), ranged from 4.16 to 5.89 across samples and could best be predicted by pH, followed by total porosity, fraction of pyrolizable carbon, and pore size distribution index. The pH alone explained 36% of the variation in H between samples. Hierarchical clustering identified three prokaryotic clusters highly correlated with pH. A weak correlation was found between differences in community composition (beta diversity) and geographic distance (r = 0.15, p &lt; 0.001). However, pH was also the main driver of beta diversity, explaining 11% of the variation. At the same time, models including additional variables only had marginally better explanatory power. In conclusion, pH was the predominant driver of prokaryotic alpha and beta diversity across land-use types in lowland soils.

Grasslands are estimated to cover about 40% of the earth’s land area and are primarily used for grazing. Despite their importance globally, there is a paucity of information on long-term grazing effects on the soil microbiome. We used a 68-year-old grazing experiment to determine differences in the soil permanganate-oxidizable C (POXC), microbial biomass C (MBC), the soil prokaryotic (bacterial and archaeal) community composition and enzyme activities between no-grazing, light grazing and heavy grazing, i.e. 0, 1.2 and 2.4 animal unit months (AUM) ha−1. The grazing effects were determined in spring and fall grazing. Light grazing had little effect on soil MBC and the composition and diversity of prokaryotic communities in either grazing season, but the effects of heavy grazing depended on the grazing season. In spring, heavy grazing increased the relative abundances of copiotrophic phyla Actinomycetota, Bacillota and Nitrososphaerota, along with soil POXC contents but decreased those of oligotrophic phyla Acidobacteriota, Verrucomicrobiota and Nitrospirota. This difference in responses was not observed in fall, when grazing reduced soil POXC, MBC and the relative abundances of most phyla. The β-diversity analysis showed that the prokaryotic community structure under heavy grazing was different from those in the control and light grazing treatments, and α-diversity indices (except the Shannon index) were highest under heavy grazing in both grazing seasons. The activities of P-mobilizing and S-mobilizing soil enzymes decreased with increasing cattle stocking rate in both seasons, but the activities of the enzymes that mediate C and N cycling decreased only in the fall. The genus RB41 (phylum Acidobacteriota) was one of two core bacterial genera, and its relative abundance was positively correlated with the activity of the S-mobilizing enzyme. Therefore, light grazing is recommended to reduce negative effects on the grassland soil microbiome and its activity, and the grazing season should be considered when evaluating such grazing effects.

Prokaryotes are the most abundant living organisms in the marine environment. They contribute to primary production and the recycling of its products. Collectively they influence the marine element cycles of carbon along with elements like nitrogen and sulfur. However, much remains to learn of the functional characteristics of microbial communities carrying out these processes, and how different communities respond to changing environmental conditions in space and time.The composition of marine prokaryotic communities is known to change in a seasonal manner, but how seasonality influences their gene expression or “activity” remains largely unknown. In this thesis I investigate the relationship between prokaryotic activity, relative gene expression, and seasonality using time series field data on gene expression combined with reference genomes of prokaryotic populations (metagenome assembled genomes, MAGs). This revealed pronounced seasonal succession in overall transcriptional dynamics. Importantly, roughly half of the 50 populations with highest relative abundance in transcription altered their transcriptional profiles across seasons. Thus, changes in relative gene expression on the annual scale is explained by community turnover and modulation of activity within populations. Characterization of a MAG representative of the filamentous cyanobacterial genus Aphanizomenon that forms summer blooms in the Baltic Proper, highlighted seasonal patterns in transcription of genes underlying key prokaryotic activities. This included genes related to photosynthesis (different genes expressed in different seasons), nitrogen- fixation (expression peaking in summer) and oxidative stress (peaking in winter). A mesocosm study in the Bothnian Sea using temperature and nutrient manipulations simulating the winter to summer transition showed lower growth efficiency and higher maintenance respiration in winter conditions, implying larger relative losses of CO2 through respiration in winter. Additionally, temperature, nutrients, and their combination, caused separation in both prokaryotic taxonomy and transcription of metabolic pathways. Key features included archaeal transcription of ammonium oxidation in winter conditions, and Oceanospirillales central metabolisms in summer. Taken together, these results highlight the pronounced effect of seasonality on prokaryotic community gene expression and the capability of prokaryotic populations to alter their expressed genetic repertoire. This emphasizes the importance of the temporal perspective when considering how prokaryotic communities will respond to changes in environmental conditions.

One of the most prominent manifestations of climate change is the changing Arctic sea-ice regime with a reduction in the summer sea-ice extent and a shift from thicker, perennial multiyear ice towards thinner, first-year ice. These changes in the physical environment are likely to impact microbial communities, a key component of Arctic marine food webs and biogeochemical cycles. During the Norwegian young sea ICE expedition (N-ICE2015) north of Svalbard, seawater samples were collected at the surface (5m), subsurface (20 or 50m), and mesopelagic (250m) depths on 9 March, 27 April, and 16 June 2015. In addition, several physical and biogeochemical data were recorded to contextualize the collected microbial communities. Through the massively parallel sequencing of the small subunit ribosomal RNA amplicon and metagenomic data, this work allows studying the Arctic's microbial community structure during the late winter to early summer transition. Results showed that, at compositional level, Alpha- (30.7%) and Gammaproteobacteria (28.6%) are the most frequent taxa across the prokaryotic N-ICE2015 collection, and also the most phylogenetically diverse. Winter to early summer trends were quite evident since there was a high relative abundance of thaumarchaeotes in the under-ice water column in late winter while this group was nearly absent during early summer. Moreover, the emergence of Flavobacteria and the SAR92 clade in early summer might be associated with the degradation of a spring bloom of Phaeocystis. High relative abundance of hydrocarbonoclastic bacteria, particularly Alcanivorax (54.3%) and Marinobacter (6.3%), was also found. Richness showed different patterns along the depth gradient for prokaryotic (highest at mesopelagic depth) and protistan communities (higher at subsurface depths). The microbial N-ICE2015 collection analyzed in the present study provides comprehensive new knowledge about the pelagic microbiota below drifting Arctic sea-ice. The higher microbial diversity found in late winter/early spring communities reinforces the need to continue with further studies to properly characterize the winter microbial communities under the pack-ice.

Agriculture is undergoing an agroecological transition characterized by adopting new practices to reduce chemical fertilizer inputs. In this context, digestates are emerging as sustainable substitutes for mineral fertilizers. However, large-scale application of digestates in agricultural fields requires rigorous studies to evaluate their long-term effects on soil microbial communities, which are crucial for ecosystem functioning and resilience. This study presents provides a comparative analysis in long-term field conditions of fertilization strategies combining annual applications of raw digestate with biennial applications of different organic waste products (OWPs)-biowaste compost (BIO), farmyard manure (FYM), and urban sewage sludge (SLU)-and compares them to combinations of the same OWPs with mineral fertilizers. The cumulative effects of repeated OWP applications, paired with two nitrogen sources-organic (digestate) and chemical (mineral fertilizer)-were assessed through soil physicochemical and microbial analyses. We hypothesized that the combined effect varied according to the N-supply sources and that this effect also depended on the type of OWP applied. Soil microbial communities were characterized using high-throughput sequencing targeting 16S and 18S ribosomal RNA genes, following DNA extraction from soil samples collected in 2022, six years after the initial digestate application. The results indicated that combining OWPs rich in stable and recalcitrant organic matter, such as BIO and FYM, with raw digestate, offers an improved fertilization practice. This approach maintains soil organic carbon (SOC) levels, increases soil phosphorus and potassium content, and stimulates microbial communities differently than nitrogen supplied via mineral fertilizers. While microbial biomass showed no significant variation across treatments, microbial diversity indices exhibited differences based on the type of OWP and nitrogen source. The fertilization strategies moderately influenced prokaryotic and fungal community structures, with distinct patterns depending on the OWP and nitrogen source. Notably, fungal communities responded more strongly to treatment variations than prokaryotic communities. This study provides new insights into the cumulative effects of substituting mineral fertilizers with digestates on soil microbial communities and soil physicochemical parameters. The sustainable development of agroecosystems significantly depends on a better understanding of the complex responses of soil microbial communities to different fertilization regimes. Future research should continue to assess the long-term impact of digestate application on soil microbiota in real agronomic field conditions, considering associated agricultural practices.

Plastic properties affect the composition of prokaryotic and eukaryotic communities and further regulate the ARGs in their surface biofilms

The microbial ecology of acidic mine and sulfide cave ecosystems is well characterised with respect to aquatic communities, typically revealing low taxonomic complexity and dominance by a relatively limited number of cosmopolitan acidophilic bacterial and archaeal taxa. Whilst pH, temperature, and geochemistry are recognised drivers of diversity in these ecosystems, the specific question of a possible influence of substratum mineralogy on microbial community composition remains unanswered. Here we address this void, using 81 subterranean mineral samples from a low temperature abandoned, acidic, sulfide ore mine system at Mynydd Parys (Parys Mountain in English), Wales, UK. Four primary and 15 secondary minerals were identified via x-ray diffraction, each sample containing a maximum of five and an average of two minerals. The mineralogy of primary (e.g. pyrite and quartz) and secondary (e.g. melanterite and pisanite) minerals was significantly correlated with prokaryotic community structure at multiple taxonomic levels, implying that the mineralosphere effect reported in less extreme terrestrial environments is also implicated in driving prokaryotic community composition in extremely acidic, base metal-bearing sulfide mineralisation at Mynydd Parys. Twenty phyla were identified, nine of which were abundant (mean relative abundance >1%). While taxa characteristic of acidic mines were detected, for example Leptospirillum (phylum Nitrospirae), Acidithiobacillus (phylum Proteobacteria), Sulfobacillus (phylum Firmicutes) and Ferroplasma (phylum Euryarchaeota), their abundance in individual samples was highly variable. Indeed, in the majority of the 81 samples investigated the abundance of these and other typical acidic mine taxa was low, with 25% of samples devoid of sequences from recognised acidic mine taxa. Most notable amongst the bacterial taxa not previously reported in such environments were the recently cultivated Muribaculaceae family (phylum Bacteroidetes), which often dominated Mynydd Parys samples regardless of their mineralogical content. Our results pose further questions regarding the mechanisms by which taxa not previously reported in such extreme environments appear to survive in Mynydd Parys, opening up research pathways for exploring the biodiversity drivers underlying microbial community composition and function in extremely acidic mine environments.

The prokaryotic abundance and diversity in three cold, oligotrophic Patagonian lakes (Témpanos, Las Torres and Mercedes) in the northern region Aysén (Chile) were compared in winter and summer using 16S rRNA fluorescence in situ hybridization and PCR-denaturing gradient gel electrophoresis technique. Prokaryotic abundances, numerically dominated by Bacteria, were quite similar in the three lakes, but higher in sediments than in waters, and they were also higher in summer than in winter. The relative contribution of Archaea was greater in waters than in sediments, and in winter rather than in summer. Despite the phylogenetic analysis indicated that most sequences were affiliated to a few taxonomic groups, mainly referred to Proteobacteria (consisting of Beta-, Alpha- and Gammaproteobacteria) and Euryarchaeota (mainly related to uncultured methanogens), their relative abundances differed in each sample, resulting in different bacterial and archaeal assemblages. In winter, the abundance of the dominant bacterial phylotypes were mainly regulated by the increasing levels of total organic carbon in waters. Archaeal abundance and richness appeared mostly influenced by pH in winter and total nitrogen content in summer. The prokaryotic community composition at Témpanos lake, located most northerly and closer to a glacier, greatly differed in respect to the other two lakes. In this lake was detected the highest bacterial diversity, being Betaproteobacteria the most abundant group, whereas Alphaproteobacteria were distinctive of Mercedes. Archaeal community associated with sediments was mainly represent by members related to the order of Methanosarcinales at Mercedes and Las Torres lakes, and by Crenarchaeota at Témpanos lake. Our results indicate that the proximity to the glacier and the seasonality shape the composition of the prokaryotic communities in these remote lakes. These results may be used as baseline information to follow the microbial community responses to potential global changes and to anthropogenic impacts.

Soil solarization and biological control are two management strategies that have been used globally to manage soil‐borne plant pathogens. However, the broader effects of these strategies on soil microbial communities have not been well described. Soil prokaryotic and fungal communities were investigated by environmental DNA amplicon sequencing as part of field trials conducted in San Rafael, CA, and in Corvallis, OR. We examined microbial community changes following soil solarization, amendment with the biocontrol agent Trichoderma asperellum (TA), or solarization followed by application of the biocontrol agent. Soil solarization caused significant changes to prokaryotic and fungal communities by reducing species richness and diversity. Soil water potential was determined to be a significant factor affecting the prokaryotic community. Application of TA to solarized or nonsolarized soil did not significantly alter the microbial communities. However, solarization resulted in diminished microbial densities that appeared to enhance subsequent establishment of the biocontrol agent. This study revealed how specific environmental variables of heat intensity and soil moisture contribute to changes in the abundance of individual taxa and taxonomic groups.