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The neurotoxin methylmercury (MeHg) is produced mainly from the transformation of inorganic Hg by microorganisms carrying the hgcAB gene pair. Paddy soils are known to harbor diverse microbial communities exhibiting varying abilities in methylating inorganic Hg, but their distribution and environmental drivers remain unknown at a large spatial scale. Using hgcA gene amplicon sequencing, this study examined Hg-methylating communities from major rice-producing paddy soils across a transect of ∼3600 km and an altitude of ∼1300 m in China. Results showed that hgcA⁺ OTU richness was higher in tropical and subtropical paddy soils compared to temperate zones. Geobacteraceae, Smithellaceae, and Methanoregulaceae were identified as the dominant hgcA⁺ families associated with MeHg production, collectively accounting for up to 77% of total hgcA⁺ sequences. Hierarchical partitioning analyses revealed that pH was the main driver of hgcA genes from Geobacteraceae (14.8%) and Methanoregulaceae (16.3%), while altitude accounted for 21.4% of hgcA genes from Smithellaceae. Based on these environmental preferences, a machine-learning algorithm was used to predict the spatial distribution of these dominant hgcA⁺ families, thereby providing novel insights into important microbial determinants for improved prediction of MeHg production in paddy soils across China.

Human activities drive a wide range of environmental pressures, including habitat change, pollution and climate change, resulting in unprecedented effects on biodiversity1,2. However, despite decades of research, generalizations on the dimensions and extent of human impacts on biodiversity remain ambiguous. Mixed views persist on the trajectory of biodiversity at the local scale3 and even more so on the biotic homogenization of biodiversity across space4,5. We compiled 2,133 publications covering 97,783 impacted and reference sites, creating an unparallelled dataset of 3,667 independent comparisons of biodiversity impacts across all main organismal groups, habitats and the five most predominant human pressures1,6. For all comparisons, we quantified three key measures of biodiversity to assess how these human pressures drive homogenization and shifts in composition of biological communities across space and changes in local diversity, respectively. We show that human pressures distinctly shift community composition and decrease local diversity across terrestrial, freshwater and marine ecosystems. Yet, contrary to long-standing expectations, there is no clear general homogenization of communities. Critically, the direction and magnitude of biodiversity changes vary across pressures, organisms and scales at which they are studied. Our exhaustive global analysis reveals the general impact and key mediating factors of human pressures on biodiversity and can benchmark conservation strategies.

1. The impacts of environmental change on Lake Biwa have been explored for decades, with water monitoring and palaeolimnological studies revealing how environmental forcing, including climate warming, eutrophication, water level manipulation and human manipulation of fish populations, has influenced the food web of Lake Biwa. However, these studies have rarely accounted for microbial food-web components. This knowledge gap is mostly due to the lack of time series spanning more than a couple of decades, coupled with the high taxonomical expertise required to identify organisms belonging to very diverse groups.
2. The use of a sedimentary DNA approach allows for the reconstruction of past changes in the diversity, composition and structure of the microbial eukaryotic community of aquatic systems. The application of 18S metabarcoding has been proven successful to describe the response of unicellular eukaryotes (protists) and aquatic fungi in lake ecosystems, encompassing a large taxonomic and functional diversity such as phototrophs, heterotrophs and mixotrophs.
3. We applied 18S metabarcoding to 31 sediment core samples from Lake Biwa, spanning the past 100 years and explored the response of microbial eukaryotic communities to changes in multiple environmental stressors, including nutrient levels, lake water level, climate, as well as fish and zooplankton biomass for the period 1973–2010.
4. We found that the manipulation of the water level and changes in fish community composition were the primary factors impacting (indirectly) the structure of the lake microbial eukaryotic community with minor, but significant, effects of climate warming and phosphorus levels. Co-occurrence network analysis highlighted the potential food web impacts on the microbial eukaryotic community, suggesting that organisms from this compartment were impacted by both bottom-up and top-down processes.

Human impacts on Earth's atmosphere, hydrosphere, litosphere and biosphere are so significant as to naming a new geological epoch, the Anthropocene. Lakes and their biota are highly sensitive to environmental changes. Among aquatic organisms, microbial eukaryotes play fundamental roles associated with lake ecosystem functioning, food webs, nutrient cycling, and pollutant degradation. However, the response of lake microbial eukaryotic community during the Anthropocene to changes in environmental conditions remain poorly understood. Here, we applied a 18S metabarcoding approach to sedimentary DNA to reconstruct the temporal dynamics of microbial eukaryotic community over the past 160 years. We investigated the influence of environmental conditions and of biotic interactions on the microbial eukaryotes in Sihailongwan Maar Lake, one of the candidate sites of Global boundary Stratotype Section and Point (GSSP) for demarcation of the Anthropocene. Microbial eukaryotes were dominated by dinoflagellates, chlorophytes, ciliates, pirsoniales, rotifers, ochrophytes, apicomplexans and cercozoans that were divided into four functional groups that are photoautotrophs, mixotrophs, consumers and parasites. The predominance of phototrophs and their strong associations with organisms from other trophic levels, confirmed their crucial roles in nutrient cycling, energy flows and ecosystem services in freshwater ecosystems. Abrupt changes in the 1950s in microbial eukaryotic diversity and composition were consistent with changes observed in the pollutants emissions i.e., heavy metals, combustion indices (spheroidal carbonaceous particles, polycyclic aromatic hydrocarbon, Soot F14C), radioactivity indicators (239,240Pu, 129I/127I), nutrients (total organic carbon, total nitrogen, phosphorus), and temperature. Statistical analysis revealed that anthropogenic drivers controlled the temporal dynamic of microbial eukaryotic community. Our findings provide additional biostratigraphy evidence of the impact of environmental change on this lake biota, which further supports the value of this system to characterize the Anthropocene.

Subsurface microorganisms make up the majority of Earth's microbial biomass, but ecological processes governing surface communities may not explain community patterns at depth because of burial. Depth constrains dispersal and energy availability, and when combined with geographic isolation across landscapes, may influence community assembly. We sequenced the 16S rRNA gene of bacteria and archaea from 48 sediment cores across 36 lakes in four disconnected mountain ranges in Wyoming, USA and used null models to infer assembly processes across depth, spatial isolation, and varying environments. Although we expected strong dispersal limitations across these isolated settings, community composition was primarily shaped by environmental selection. Communities consistently shifted from domination by organisms that degrade organic matter at the surface to methanogenic, low-energy adapted taxa in deeper zones. Stochastic processes—like dispersal limitation—contributed to differences among lakes, but because these effects weakened with depth, selection processes ultimately governed subsurface microbial biogeography.

Investigating the occurrence of antibiotic-resistance genes (ARGs) in sedimentary archives provides opportunities for reconstructing the distribution and dissemination of historical (i.e., non-anthropogenic origin) ARGs. Although ARGs in freshwater environments have attracted great attention, historical variations in the diversity and abundance of ARGs over centuries to millennia remain largely unknown. In this study, we investigated the vertical change patterns of bacterial communities, ARGs and mobile genetic elements (MGEs) found in sediments of Lake Chenghai spanning the past 600 years. Within resistome preserved in sediments, 177 ARGs subtypes were found with aminoglycosides and multidrug resistance being the most abundant. The ARG abundance in the upper sediment layers (equivalent to the post-antibiotic era since the 1940s) was lower than those during the pre-antibiotic era, whereas the ARG diversity was higher during the post-antibiotic era, possibly because human-induced lake eutrophication over the recent decades facilitated the spread and proliferation of drug-resistant bacteria. Statistical analysis suggested that MGEs abundance and the bacterial community structure were significantly correlated with the abundance and diversity of ARGs, suggesting that the occurrence and distribution of ARGs may be transferred between different bacteria by MGEs. Our results provide new perspectives on the natural history of ARGs in freshwater environments and are essential for understanding the temporal dynamics and dissemination of ARGs.

Antibiotic Resistance Genes (ARGs) are widespread in freshwater environments and represent a concealed threat to public health and aquatic eco-system safety. To date, only a limited number of studies have investigated the historical distribution of ARGs and their hosts through the analysis of freshwater sedimentary archives. This research gap constrains our comprehensive of the mechanisms underlying natural bacterial resistance formation during pre-antibiotic era (prior to the 1940s) and the development of human-induced bacterial resistance in post-antibiotic era (since the 1940s). In this study, we examined the vertical distribution patterns of ARGs and their associated hosts within a sedimentary core from a eutrophic lake, employing shotgun sequencing methodology. The findings revealed a marked increase in ARG diversity during post-antibiotic era, and the predominant ARG types identified included those conferring resistance to multidrug, bacitracin, macrolide-lincosamide-streptogramin, beta-lactam, tetracycline, fluoroquinolone, glycopeptide and aminoglycoside, collectively accounting for 78.3%-85.6% of total ARG abundance. A total of 127 ARG subtypes were identified in samples, and 48 ARG subtypes shared across vertical sediment resistome profile with two of them, bacA and bcrA, occurring only in post-antibiotic era. Further, 137 metagenome-assembled genomes (83 species belonging to 12 phyla) were identified as ARG hosts, mainly belonging to the phyla Proteobacteria, Nitrospirota, Chloroflexota, Bacteroidota, Actinobacteriota, Cyanobacteria, and Firmicutes. Significant correlation was found between the diversity of ARG and the concentrations of organic matter and heavy metals, suggesting a common source of contamination. Aside the fact that human-induced eutrophication is a forcing factor acting in parallel to increase ARGs releases in water systems, both being indicators of increased urbanization in the catchment, eutrophication may significantly increase bacterial activity, thereby facilitating the spread of antibiotic-resistant bacteria in environment. This study reveals the marked increased in ARG diversity with the onset of antibiotic use by human societies with potential impact of aquatic ecosystem.

Aquatic sediments harbour a diverse array of microorganisms that drive organic matter recycling, carbon sequestration and greenhouse gases (e.g., CO2, CH4, N2O) emissions. Although largely studied in water columns, vertical profiles of the diversity and composition of prokaryotic communities (i.e., Bacteria and Archaea) in aquatic sediments are still rare. More specifically, much remains to be learnt about their vertical distribution in lake sediments and how environmental conditions at the time of burial have impacted their diversity and composition.

We investigated the vertical distribution of prokaryotic community with 16S rRNA gene quantitative (q)PCR and metabarcoding approaches applied to 93 sediment layers collected in a 2-m-long sediment core from the eutrophic alkaline Lake Chenghai in subtropical China. We aimed to study the diversity, composition and structure distribution of the prokaryotic community as well as environmental factors influencing it.

Bacterial abundance was found to decrease with sediment depth although the richness of both bacterial and archaeal assemblages slightly increased with sediment depth. In terms of composition, a strongly stratified sediment–depth pattern was observed in which Proteobacteria, Desulfobacterota, Bacteroidota and Verrucomicrobiota dominated the inventories in the surface sediment layers, whereas Chloroflexi, Spirochaetota, Planctomycetota, Crenarchaeota were more abundant in the deep sediment layers. Organic matter contents and sources were identified as major factors shaping the structure of the prokaryotic community.

Overall, our study provides new evidence about how lake sediment's prokaryotic community are linked to external sources of energy. This complement existing data from other lake systems towards a better understanding of sediment prokaryotic community's contribution to biogeochemical cycle in lakes.

Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.

Anthropogenic-driven environmental change, including current climate warming, has influenced lake ecosystems globally during the Anthropocene. Phytoplankton are important indicators of environmental changes in lakes and play a fundamental role in maintaining the functioning and stability of these ecosystems. However, the extent to which lake phytoplankton were affected by anthropogenic or climatic forces during the Anthropocene remains unclear. Here, we investigated the 160-yr-long dynamics of the phytoplankton community (cyanobacteria and eukaryotic microalgae) in response to anthropogenic forcing in Sihailongwan Maar Lake—a candidate for a Global boundary Stratotype Section and Point for demarcation of the Anthropocene—using DNA metabarcoding and traditional paleolimnological approaches. Our results show a significant decline in phytoplankton diversity and an abrupt shift in community composition around the 1950s, corresponding to the beginning of the “Great Acceleration” period. Specifically, phytoplankton taxa coexistence patterns, niche differentiation, and assembly mechanisms changed significantly after the 1950s. Overall, increases in air temperature and anthropogenic forcing appear to be the dominant controls for community reorganization and diversity decline of the phytoplankton from this deep maar lake. A neutral community model suggests that phytoplankton community composition was mainly controlled by stochastic processes before the 1950s; however, as time progressed, deterministic effects driven by anthropogenic global warming increased. The results of this study imply that anthropogenic perturbations have led to a loss of phytoplankton diversity and a further decline in ecological resilience in deep lakes, with likely knock-on effects on the productivity and function of lake ecosystems.