OBJECTIVE: Microbial community functioning can be highly dynamic over time. Identifying and understanding biotic factors that control functional stability is of significant interest for natural and engineered communities alike. Using plant litter decomposing communities as a model system, this study examined the stability of ecosystem function over time following repeated community transfers. By identifying microbial community features that are associated with stable ecosystem functions, microbial communities can be manipulated in ways that promote the consistency and reliability of the desired function, improving outcomes and increasing the utility of microorganisms.

The decomposition and utilization of plant-derived carbon by microorganisms and carbon fixation are crucial pathways for enhancing soil organic carbon (SOC) storage. However, a gap remains in our understanding of the impact of microorganisms on the decomposition of plant-derived carbon and their capacity for carbon fixation in crop rotation systems. Based on a 12-year experiment with wheat-maize (WM), wheat-cotton (WC), and wheat-soybean (WS) rotations, the microbial communities and carbon cycle function were investigated. The results indicated that WS rotation significantly increased SOC content compared to WM and WC. In addition, a significant increase was observed in microbially available carbon and microbial biomass carbon in the WS soil compared with those in the others. Further analysis of the microbial community factors that influenced SOC content revealed that WS rotation, in contrast to WM rotation, enhanced the diversity and richness of bacteria and fungi. Analysis of microbial carbon decomposition functions revealed an increase in starch, lignin, and hemicellulose decomposition genes in the WS soil compared to the others. The changes in carbon decomposition genes were primarily attributed to six bacterial genera, namely Nocardioides, Agromyces, Microvirga, Skermanella, Anaeromyxobacter, and Arthrobacter, as well as four fungal genera, namely Dendryphion, Staphylotrichum, Apiotrichum, and Abortiporus, which were significantly influenced by the crop rotation systems. In addition, microbial carbon fixation-related genes such as ACAT, IDH1, GAPDH, rpiA, and rbcS were significantly enriched in WS. Species annotation of differential carbon fixation genes identified 18 genera that play a role in soil carbon fixation variation within the crop rotation systems. This study highlights the impact of crop rotation systems on SOC content and alterations in specific microbial communities on carbon cycle function.

Dissimilatory iron reduction (DIR) coupled with carbon cycling is increasingly being recognized as an influential process in freshwater wetland soils and sediments. The role of DIR in organic matter (OM) mineralization, however, is still largely unknown in lake sediment environments. In this study, we clarified rates and pathways of OM mineralization in two shallow lakes with seasonal hydrological connectivity and different eutrophic situations. We found that in comparison with the domination of DIR (55%) for OM mineralization in Lake Xiaoxingkai, the contribution of methanogenesis was much higher (68%) in its connected lake (Lake Xingkai). The differences in rates and pathways of sediment OM mineralization between the two lakes were attributed to higher concentrations of carbonate associated iron oxides (Fecarb) in Lake Xiaoxingkai compared to Lake Xingkai (P = 0.002), due to better deposition mixing, more contributions of terrigenous detrital materials, and higher OM content in Lake Xiaoxingkai. Results of structural equation modeling showed that Fecarb and total iron content (TFe) regulated 25% of DIR in Lake Xiaoxingkai and 76% in Lake Xingkai, accompanied by a negative effect of TFe on methanogenesis in Lake Xingkai. The relative abundance and diversity of Fe-reducing bacteria were significantly different between the two lakes, and showed a weak effect on sediment OM mineralization. Our findings emphasize the role of iron minerals and geochemical characterizations in regulating rates and pathways of OM mineralization, and deepen the understanding of carbon cycling in lake sediments.

Climate influences near-surface biogeochemical processes and thereby determines the partitioning of carbon dioxide (CO2) in shale, and yet the controls on carbon (C) weathering fluxes remain poorly constrained. Using a dataset that characterizes biogeochemical responses to climate forcing in shale regolith, we implement a numerical model that describes the effects of water infiltration events, gas exchange, and temperature fluctuations on soil respiration and mineral weathering at a seasonal timescale. Our modeling approach allows us to quantitatively disentangle the controls of transient climate forcing and biogeochemical mechanisms on C partitioning. We find that ~3% of soil CO2 (1.02 mol C/m2/y) is exported to the subsurface during large infiltration events. Here, net atmospheric CO2 drawdown primarily occurs during spring snowmelt, governs the aqueous C exports (61%), and exceeds the CO2 flux generated by pyrite and petrogenic organic matter oxidation (~0.2 mol C/m2/y). We show that shale CO2 consumption results from the temporal coupling between soil microbial respiration and carbonate weathering. This coupling is driven by the impacts of hydrologic fluctuations on fresh organic matter availability and CO2 transport to the weathering front. Diffusion-limited transport of gases under transient hydrological conditions exerts an important control on CO2(g) egress patterns and thus must be considered when inferring soil CO2 drawdown from the gas phase composition. Our findings emphasize the importance of seasonal climate forcing in shaping the net contribution of shale weathering to terrestrial C fluxes and suggest that warmer conditions could reduce the potential for shale weathering to act as a CO2 sink.

The Qinghai-Tibetan Plateau harbors rich and diverse wetlands that provide multiple ecological functions simultaneously. Although the relationships between biodiversity and wetland functioning have been well studied in recent decades, the links between the multiple features of plant and microbial communities and soil multifunctionality (SMF) remain unknown in the high-altitude wetlands that are extremely sensitive to human disturbance. Here, using the single function, averaging, weighted, and multiple-threshold methods, we calculated the SMF of Qinghai-Tibetan wetlands based on 15 variables associated with soil nutrient status, nutrient cycle, and greenhouse gas emission. We then related SMF to multidimensional (species, phylogenetic, and functional) diversity of plants and soil microorganisms and microbial network modules. The results showed that plant diversity explained more variance in SMF than soil microbial diversity, and plant species richness and phylogenetic distance were positive predictors of SMF. Bacterial network modules were more positively related to SMF than fungal network modules, and the alpha diversity of bacterial network modules contributed more to SMF than the diversity of the whole bacterial community. Pediococcus, Hirsutella, and Rhodotorula were biomarkers for SMF and had significant relationships with nitrogen mineralization and greenhouse gas emissions. Together, these results highlight the importance of plant diversity and bacterial network modules in determining the SMF, which are crucial to predicting the response of ecosystem functioning to biodiversity loss under intensifying anthropogenic activities.

Organophosphorus pesticides (OPPs) are important chemical stressors in aquatic ecosystems, and they attract increasing more attentions recently. However, the impacts of different OPPs on carbon cycling remain unclear, particularly for those functional-yet-uncultivable microbes. This study investigated the change in lake aquatic microbial communities in the presence of dichlorvos, monocrotophos, omethoate and parathion. All OPPs significantly inhibited biomass (p < 0.05) and the expression of carbon cycle-related cbbLG gene (p < 0.01), and altered aquatic microbial community structure, interaction, and assembly. Variance partitioning analysis showed a stronger impact of pesticide type on microbial biomass and community structure, where pesticide concentration played more significant roles in carbon cycling. From analysis of cbbLG gene and PICRUSt2, Luteolibacter and Verrucomicrobiaceae assimilated inorganic carbon through Wood-Ljungdahl pathway, whereas it was Calvin-Benson-Bassham cycle for Cyanobium PCC-6307. This work provides a deeper insight into the behavior and mechanisms of microbial community change in aquatic system in response to OPPs, and explicitly unravels the impacts of OPPs on their carbon-cycling functions.

We report the draft genome sequence of marine bacteria, Pseudomonas sp. XK-1. Strain XK-1 could facilitate Mn(II) oxidation with lignin as the sole carbon source. The genome length of XK-1 is 4,751,776 bp, with a G + C content of 62.61%. Genome analyses reveal the carbon and manganese cycling driven by bacteria.

Molecular observational tools are useful for characterizing the composition and genetic endowment of microbial communities but cannot measure fluxes, which are critical for the understanding of ecosystems. To overcome these limitations, we used a mechanistic inference approach to estimate dissolved organic carbon (DOC) production and consumption by phytoplankton operational taxonomic units and heterotrophic prokaryotic amplicon sequence variants and inferred carbon fluxes between members of this microbial community from Western English Channel time-series data. Our analyses focused on phytoplankton spring and summer blooms, as well as bacteria summer blooms. In spring blooms, phytoplankton DOC production exceeds heterotrophic prokaryotic consumption, but in bacterial summer blooms heterotrophic prokaryotes consume three times more DOC than produced by the phytoplankton. This mismatch is compensated by heterotrophic prokaryotic DOC release by death, presumably from viral lysis. In both types of summer blooms, large amounts of the DOC liberated by heterotrophic prokaryotes are reused through internal recycling, with fluxes between different heterotrophic prokaryotes being at the same level as those between phytoplankton and heterotrophic prokaryotes. In context, internal recycling accounts for approximately 75% and 30% of the estimated net primary production (0.16 vs 0.22 and 0.08 vs 0.29 μmol l-1 d-1) in bacteria and phytoplankton summer blooms, respectively, and thus represents a major component of the Western English Channel carbon cycle. We have concluded that internal recycling compensates for mismatches between phytoplankton DOC production and heterotrophic prokaryotic consumption, and we encourage future analyses on aquatic carbon cycles to investigate fluxes between heterotrophic prokaryotes, specifically internal recycling.

Plastics in aquatic ecosystems rapidly undergo biofouling, giving rise to a new ecosystem on their surface, the \'plastisphere.\' Few studies quantify the impact of plastics and their associated community on ecosystem traits from biodiversity and functional traits to metabolic function. It has been suspected that impacts on ecosystems may depend on its state but comparative studies of ecosystem responses are rare in the published literature. We quantified algal biomass, bacterial and algal biodiversity (16S and 18S rRNA), and metabolic traits of the community growing on the surface of different plastic polymers incubated within rivers of the Lower Mekong Basin. The rivers selected have different ecological characteristics but are similar regarding their high degree of plastic pollution. We examined the effects of plastics colonized with biofilms on ecosystem production, community dark respiration, and the epiplastic community\'s capability to influence nitrogen, phosphorus, organic carbon, and oxygen in water. Finally, we present conceptual models to guide our understanding of plastic pollution within freshwaters. Our findings showed limited microalgal biomass and bacterial dominance, with potential pathogens present. The location significantly influenced community composition, highlighting the role of environmental conditions in shaping community development. When assessing the effects on ecosystem productivity, our experiments showed that biofouled plastics led to a significant drop in oxygen concentration within river water, leading to hypoxic/anoxic conditions with subsequent profound impacts on system metabolism and the capability of influencing biogeochemical cycles. Scaling our findings revealed that plastic pollution may exert a more substantial and ecosystem-altering impact than initially assumed, particularly in areas with poorly managed plastic waste. These results highlighted that the plastisphere functions as a habitat for biologically active organisms which play a pivotal role in essential ecosystem processes. This warrants dedicated attention and investigation, particularly in sensitive ecosystems like the Mekong River, which supports a rich biodiversity and the livelihoods of 65 million people.

Brownification in aquatic ecosystems under global change has attracted attention. The composition and quantity of dissolved organic matter transported from various land use types to lakes differ significantly, causing varying ecological effects of lake brownification by region. Bacterial communities make a significant contribution to the material cycle of ecosystems and are sensitive to environmental changes. In this study, a series of mesocosm systems were used to simulate forest lakes and urban lakes with different degrees of brownification, and a high-throughput amplicon sequencing technique was used to explore the changes in the composition, structure, and function of bacterial communities in shallow lakes undergoing brownification. Principal coordinate analysis (PCoA) and Jensen‒Shannon distance typing analysis both indicated significant differences in bacterial communities between forest lakes and urban lakes. The α diversity of bacterial communities in urban lakes increased with the degree of brownification. However, whether forest lakes or urban lakes, brownification increased the abundance of carbon cycling-related bacterial phyla (Proteobacteria, Poribacteria, and Chloroflexi) and nitrogen cycling-related bacterial genera (Microbacteriaceae, Limnohabitans, Comamonadaceae, Bacillus, and Rhizobiales_Incertae_Sedis). Additionally, the carbon and nitrogen cycling functions of bacterial communities in forest lakes are dominant, while those in urban lakes are dominated by functions related to light. Our study has preliminarily revealed that lake brownification promotes the growth of carbon and nitrogen cycling microorganisms, providing a new paradigm for understanding the response of lake ecosystems in different catchment areas to environmental changes and the carbon and nitrogen cycling processes in shallow lake ecosystems.