Greenhouse gases and biogeochemical diel fluctuations in a high-altitude wetland

Spatial Patterns of Microbial Communities in Intertidal Sediments of the Yellow River Estuary, China

Estuarine ecosystems are among the most important natural ecosystems on Earth and contribute substantially to human survival and development. The Yellow River Estuary (YRE) is the second largest estuary in China. Microbial communities play an essential role in the material cycle and energy flow in estuarine ecosystems. To date, our knowledge of the spatial patterns of bacterial and archaeal communities is limited. In this study, we investigated the spatial profile of bacterial and archaeal communities and their co-occurrence patterns, functional roles, and environmental driving factors in the intertidal sediments of the YRE from June to July, 2019. The results showed that Proteobacteria, Bacteroidetes, Chloroflexi, and Planctomycetes were the dominant bacterial phyla, whereas Nanoarchaeaeota, Euryarchaeota and Thaumarchaeota were the dominant archaeal phyla in the intertidal sediments of the YRE. Diversity indices and differential abundance analyses revealed significant (p < 0.05) differences in the bacterial and archaeal communities in the intertidal sediments of the YRE. Bacterial communities demonstrated distinct correlations with heavy metals and pollutants. Six archaeal genera exhibited co-occurrence patterns with bacterial genera. Functions associated with sulfur cycles, disease, and pollution were specific to bacterial communities. This study presents a detailed outline of the spatial patterns of microbial communities in the YRE, enriching our understanding of microbial ecology, especially of bacteria and archaea.

Protist communities of microbial mats from the extreme environments of five saline Andean lagoons at high altitudes in the Atacama Desert

Introduction

Heterotrophic protists colonizing microbial mats have received little attention over the last few years, despite their importance in microbial food webs. A significant challenge originates from the fact that many protists remain uncultivable and their functions remain poorly understood.

Methods

Metabarcoding studies of protists in microbial mats across high-altitude lagoons of different salinities (4.3-34 practical salinity units) were carried out to provide insights into their vertical stratification at the millimeter scale. DNA and cDNA were analyzed for selected stations.

Results

Sequence variants classified as the amoeboid rhizarian Rhogostoma and the ciliate Euplotes were found to be common members of the heterotrophic protist communities. They were accompanied by diatoms and kinetoplastids. Correlation analyses point to the salinity of the water column as a main driver influencing the structure of the protist communities at the five studied microbial mats. The active part of the protist communities was detected to be higher at lower salinities (<20 practical salinity units).

Discussion

We found a restricted overlap of the protist community between the different microbial mats indicating the uniqueness of these different aquatic habitats. On the other hand, the dominating genotypes present in metabarcoding were similar and could be isolated and sequenced in comparative studies (Rhogostoma, Euplotes, Neobodo). Our results provide a snapshot of the unculturable protist diversity thriving the benthic zone of five athalossohaline lagoons across the Andean plateau.

Short-term characterisation of climatic-environmental variables and microbial community diversity in a high-altitude Andean wetland (Salar de Huasco, Chile)

Microbial community structures are shaped by geochemical factors and their interactions with the lithosphere, hydrosphere, and atmosphere through the processes of chemical mobilisation and mineralisation. High-altitude wetlands and salt flats in the central Andes are characterised by pronounced physicochemical gradients and extreme climatic conditions, representing hotspots of microbial diversity. We here hypothesise about the existence of direct relationships between the local microbiology and the climate cyclicity variables based on meteorological and biogeochemical patterns that develop over a short time scale (five years). We have here analysed the interactions between hydrometeorological and biogeochemical variables and the microbial communities of the Salar de Huasco. These results were obtained by correlating 16S cDNA and DNA gene Illumina sequences with meteorological/satellite data collected both at monitoring stations and by remote sensing between the years 2015 and 2020. The precipitation levels and flooded areas (i.e., areas covered and/or saturated with permanent water) detected in the Salar de Huasco revealed a marked hydric cyclicity that correlated seasonally with intra-annual wet and dry seasons. Overall, at this site, wet periods occurred from December to April, and dry periods from May to November. Meteorological variables such as solar radiation, air temperature, relative humidity, wind speed, atmospheric pressure, and wind direction were well-defined, showing a potential association with the hydrogeology of the area, which is directly related to the wetlands' flooded areas. Finally, the microbial presence and potentially active microbial communities were determined through the sequencing of the 16S gene (DNA and cDNA, respectively), this were associated with climatic seasonality and spatially distributed physical and chemical heterogeneity. Other non-local inter-annual scale processes, such as El Niño-Southern Oscillation (ENSO) events, modify the physical and chemical context of the wetland, thus forming unique ecological niches in the Andean Mountains.

Arbuscular Mycorrhizae Shift Community Composition of N-Cycling Microbes and Suppress Soil N2O Emission

Mycorrhizae are ubiquitous symbiotic associations between arbuscular mycorrhizal fungi (AMF) and terrestrial plants, in which AMF receive photosynthates from and acquire soil nutrients for their host plants. Plant uptake of soil nitrogen (N) reduces N substrate for microbial processes that generate nitrous oxide (N₂O), a potent greenhouse gas. However, the underlying microbial mechanisms remain poorly understood, particularly in agroecosystems with high reactive N inputs. We examined how plant roots and AMF affect N₂O emissions, N₂O-producing (nirK and nirS) and N₂O-consuming (nosZ) microbes under normal and high N inputs in conventional (CONV) and organically managed (OM) soils. Here, we show that high N input increased soil N₂O emissions and the ratio of nirK to nirS microbes. Roots and AMF did not affect the (nirK + nirS)/nosZ ratio but significantly reduced N₂O emissions and the nirK/nirS ratio. They reduced the nirK/nirS ratio by reducing nirK-Rhodobacterales but increasing nirS-Rhodocyclales in the CONV soil while decreasing nirK-Burkholderiales but increasing nirS-Rhizobiales in the OM soil. Our results indicate that plant roots and AMF reduced N₂O emission directly by reducing soil N and indirectly through shifting the community composition of N₂O-producing microbes in N-enriched agroecosystems, suggesting that harnessing the rhizosphere microbiome through agricultural management might offer additional potential for N₂O emission mitigation.

Integrating high-throughput sequencing and metabolomics to investigate the stereoselective responses of soil microorganisms to chiral fungicide cis-epoxiconazole

The use of the chiral triazole fungicide cis-epoxiconazole in agricultural production continues to increase; however, little is known about the stereoselective and toxic responses of soil microorganisms to cis-epoxiconazole in the soil microenvironment. High-throughput sequencing and metabolomics were integrated to investigate the stereoselective response of soil microbial community structure, metabolic profile to cis-epoxiconazole exposure, and the correlation between the microbiomes and different metabolites. Soil microbial community structure and soil metabolic profile were significantly altered and exhibited significant enantioselectivity. The alpha diversity (Chao, Shannon, and Simpson diversity) of bacterial and fungus was not significantly affected, whereas the beta diversity (Bray-Curtis dissimilarity and PLS-DA) of bacterial and fungus was significantly altered in treatment of cis-epoxiconazole and its enantiomers (p-value < 0.05). The variation in bacterial and fungus community structure was the highest under (+)-enantiomer exposure, followed by exposure to racemate and (-)-enantiomer. Soil metabolomic analysis revealed that exposure to high or low doses of cis-epoxiconazole and its enantiomers resulted in different degrees of reprogramming of the soil metabolic pool. The 39 significantly changed metabolites mainly included small molecular organic acids, amino acids and their intermediates, and purine and adenosine intermediates. Six metabolic pathways were significantly disrupted. Different correlation patterns were observed between the significantly altered metabolites and microbes (p-value < 0.05) by Pearson correlation-based analysis. In conclusion, as xenobiotic pollutant, epoxiconazole altered the structure and metabolism of soil microorganisms with significant stereoselectivity mainly driven by 2R, 3S-(+)-cis-epoxiconazole. This study provided a more robust assessment of the risks of epoxiconazole exposure to soil microorganisms. Given the importance of the soil environment in agricultural production, characterization of the soil microbiome and metabolome can provide new insights into the ecological risks posed by exposure to the chiral triazole pesticide cis-epoxiconazole and its enantiomers.