Temperature-mediated microbial carbon utilization in China's lakes

Mitigating sediment cadmium contamination through combining PGPR Enterobacter ludwigii with the submerged macrophyte Vallisneria natans

Sediment cadmium contamination poses risks to aquatic ecosystems. Phytoremediation is an environmentally sustainable method to mitigate cadmium contamination. Submerged macrophytes are affected by cadmium stress, but plant growth-promoting rhizobacteria (PGPR) can restore the health status of submerged macrophytes. Herein, we aimed to reduce sediment cadmium concentration and reveal the mechanism by which the combined application of the PGPR Enterobacter ludwigii and the submerged macrophyte Vallisneria natans mitigates cadmium contamination. Sediment cadmium concentration decreased by 21.59% after submerged macrophytes were planted with PGPR, probably because the PGPR colonized the rhizosphere and roots of the macrophytes. The PGPR induced a 5.09-fold increase in submerged macrophyte biomass and enhanced plant antioxidant response to cadmium stress, as demonstrated by decreases in oxidative product levels (reactive oxygen species and malondialdehyde), which corresponded to shift in rhizosphere metabolism, notably in antioxidant defence systems (i.e., the peroxidation of linoleic acid into 9-hydroperoxy-10E,12Z-octadecadienoic acid) and in some amino acid metabolism pathways (i.e., arginine and proline). Additionally, PGPR mineralized carbon in the sediment to promote submerged macrophyte growth. Overall, PGPR mitigated sediment cadmium accumulation via a synergistic plantmicrobe mechanism. This work revealed the mechanism by which PGPR and submerged macrophytes control cadmium concentration in contaminated sediment.

Submerged macrophyte restoration enhanced microbial carbon utilization in shallow lakes

Submerged macrophytes are integral to the functioning of shallow lakes through their interaction with microorganisms. However, we have a limited understanding of how microbial communities in shallow lakes respond when macrophytes are restored after being historically extirpated. Here, we explored the interactions between prokaryotic communities and carbon utilization in two lakes where submerged macrophytes were restored. We found restoration reduced total carbon in sediment by 8.9 %-27.9 % and total organic carbon by 16.7 %-36.9 % relative to control treatment, but had no effects on carbon content in the overlying water. Sediment microbial communities were more sensitive to restoration than planktonic microbes and showed enhanced utilization of simple carbon substrates, such as Tween 40, after restoration. The increase in carbon utilization was attributed to declines in the relative abundance of some genera, such as Saccharicenans and Desertimonas, which were found weakly associated with the utilization of different carbon substrates. These genera likely competed with microbes with high carbon utilization in restored areas, such as Lubomirskia. Our findings highlight how restoring submerged macrophytes can enhance microbial carbon utilization and provide guidance to improve the carbon sequestration capacity of restored shallow lakes.

Characteristics and correlation analysis of heavy metal distribution in China's freshwater aquaculture pond sediments

The concentration of heavy metals (HMs) in aquaculture pond sediments significantly affects aquatic food safety and environmental quality. The contamination characteristics, drivers and potential sources of HMs in typical bulk freshwater aquaculture pond sediments in major provinces of China were systematically investigated using a variety of methods and models. Specifically, 130 surface sediment samples were collected from the study area, and the geoaccumulation index (Igeo) and potential ecological risk index (RI) were used to jointly evaluate the characteristics of the HMs. Spearman's correlation and redundancy analysis revealed the main drivers of the HMs. Additionally, the positive matrix factorization (PMF) model and absolute principal component score-multiple linear regression (APCS-MLR) model were used to identify the sources of HMs. The results revealed that the pond sediments were safe for fish culture in most of the study areas. Aquafeed protein content is an important driver of HM concentrations in sediments. The total organic carbon (TOC) content, percentage of clay particles, and pH of the aquaculture pond sediments determined the sediment HMs enrichment abilities as 13.6 %, 52 %, and 9.8 %, respectively. Cd, a significantly enriched pollutant, posed a greater ecological risk than the other five HMs (Cr, Cu, Zn, As, and Pb). Three sources of HMs were identified, including agricultural activity (e.g., aquafeeds, pesticides, and fertilizers), industrial production, and natural sources, with contributions of 44.29 %, 36.66 %, and 19.05 %, respectively. This study provides a scientific basis for minimizing the input and accumulation of HMs in freshwater aquaculture pond sediments, and this can provide insights into the prevention and control of the ecological risks posed by HMs.

Distinct drivers of bacterial community assembly processes in riverine islands in the middle and lower reaches of the Yangtze River

Riverine islands are widespread alluvium wetlands developed in large rivers, and bacterial communities are crucial to their ecological function, yet their assembly processes are rarely addressed. The ecosystem services provided by the middle and the lower Yangtze are primarily threatened by pollution discharge from agricultural land use, and resource overutilization (e.g., embankments), respectively. Here, we assessed bacterial community assembly processes and their drivers within riverine islands in the middle Yangtze River (MR islands) and those in the lower reach (LR islands). A significant distance-decay relationship was observed, although the turnover rate was lower than that of the terrestrial ecosystem with less connectivity. Deterministic and stochastic processes jointly shaped community patterns, and the influence of stochastic increased from 26% in MR islands to 59% for those in LR islands. Meanwhile, the bacterial community in MR islands was controlled more by inorganic nitrogen availability, whereas those in LR islands were governed by pH and EC, although those factors explained a limited fraction of variation in the bacterial community. Potential indicator taxa (affiliated with Nocardioides and Lysobacter) characterized the waterway transport pollution. Overall, our study demonstrated that bacterial community dissimilarity and the importance of dispersal limitation increased concurrently along the flow direction, while distinct local factors further determined bacterial community compositions by selecting habitat-specificity taxa and particularly metabolism function. These findings enhanced our understanding of the mechanisms driving changes in bacterial communities of riverine islands subject to increased anthropogenic impacts.IMPORTANCERivers are among the most threatened ecosystems globally and face multiple stressors related to human activity. However, linkages between microbial diversity patterns and assembly processes in rivers remain unclear, especially in riverine islands developed in large rivers. Our findings reveal that distinct factors result in divergent bacterial community compositions and functional profiles in the riverine islands in the middle Yangtze and those in the lower Yangtze, with substantial differentiation in deterministic and stochastic processes that jointly contribute to bacterial community assemblages. Additionally, keystone species may play important metabolic roles in coping with human-related disturbances. This study provides an improved understanding of relationships between microbial diversity patterns and ecosystem functions under environmental changes in large river ecosystems.

Geographic distribution of bacterial communities of inland waters in China

Microorganisms are integral to freshwater ecological functions and, reciprocally, their activity and diversity are shaped by the ecosystem state. Yet, the diversity of bacterial community and its driving factors at a large scale remain elusive. To bridge this knowledge gap, we delved into an analysis of 16S RNA gene sequences extracted from 929 water samples across China. Our analyses revealed that inland water bacterial communities showed a weak latitudinal diversity gradient. We found 530 bacterial genera with high relative abundance of hgcI clade. Among them, 29 core bacterial genera were identified, that is strongly linked to mean annual temperature and nutrient loadings. We also detected a non-linear response of bacterial network complexity to the increasing of human pressure. Mantel analysis suggested that MAT, HPI and P loading were the major factors driving bacterial communities in inland waters. The map of taxa abundance showed that the abundant CL500-29 marine group in eastern and southern China indicated high eutrophication risk. Our findings enhance our understanding of the diversity and large-scale biogeographic pattern of bacterial communities of inland waters and have important implications for microbial ecology.

Understanding Salinity-Driven Modulation of Microbial Interactions: Rhizosphere versus Edaphic Microbiome Dynamics

Soil salinization poses a global threat to terrestrial ecosystems. Soil microorganisms, crucial for maintaining ecosystem services, are sensitive to changes in soil structure and properties, particularly salinity. In this study, contrasting dynamics within the rhizosphere and bulk soil were focused on exploring the effects of heightened salinity on soil microbial communities, evaluating the influences shaping their composition in saline environments. This study observed a general decrease in bacterial alpha diversity with increasing salinity, along with shifts in community structure in terms of taxa relative abundance. The size and stability of bacterial co-occurrence networks declined under salt stress, indicating functional and resilience losses. An increased proportion of heterogeneous selection in bacterial community assembly suggested salinity's critical role in shaping bacterial communities. Stochasticity dominated fungal community assembly, suggesting their relatively lower sensitivity to soil salinity. However, bipartite network analysis revealed that fungi played a more significant role than bacteria in intensified microbial interactions in the rhizosphere under salinity stress compared to the bulk soil. Therefore, microbial cross-domain interactions might play a key role in bacterial resilience under salt stress in the rhizosphere.

Long-term conservation tillage enhances microbial carbon use efficiency by altering multitrophic interactions in soil

Microbial carbon (C) use efficiency (CUE) plays a key role in soil C storage. The predation of protists on bacteria and fungi has potential impacts on the global C cycle. However, under conservation tillage conditions, the effects of multitrophic interactions on soil microbial CUE are still unclear. Here, we investigate the multitrophic network (especially the keystone ecological cluster) and its regulation of soil microbial CUE and soil organic C (SOC) under different long-term (15-year) tillage practices. We found that conservation tillage (CT) significantly enhanced microbial CUE, turnover, and SOC (P < 0.05) compared to traditional tillage (control, CK). At the same time, tillage practice and soil depth had significant effects on the structure of fungal and protistan communities. Furthermore, the soil biodiversity of the keystone cluster was positively correlated with the microbial physiological traits (CUE, microbial growth rate (MGR), microbial respiration rate (Rs), microbial turnover) and SOC (P < 0.05). Protistan richness played the strongest role in directly shaping the keystone cluster. Compared with CK, CT generally enhanced the correlation between microbial communities and microbial physiological characteristics and SOC. Overall, our results illustrate that the top-down control (the organisms at higher trophic levels affect the organisms at lower trophic levels) of protists in the soil micro-food web plays an important role in improving microbial CUE under conservation tillage. Our findings provide a theoretical basis for promoting the application of protists in targeted microbial engineering and contribute to the promotion of conservation agriculture and the improvement of soil C sequestration potential.

Warming reduces microeukaryotic diversity, network complexity and stability

Unraveling how climate warming affects microorganisms and the underlying mechanisms has been a hot topic in climate change and microbial ecology. To date, many studies have reported microbial responses to climate warming, especially in soil ecosystems, however, knowledge of how warming influences microeukaryotic diversity, network complexity and stability in lake ecosystems, in particular the possible underlying mechanisms, is largely unknown. To address this gap, we conducted 20 mesocosms spanning five temperature scenarios (26 °C, 27.5 °C, 29 °C, 30.5 °C, and 32 °C) in Lake Bosten, a hotspot for studying climate change, and investigated microeukaryotic communities using 18S rRNA gene sequencing. Our results demonstrated that warming, time, and their interactions significantly reduced microeukaryotic α-diversity (two-way ANOVA: P＜0.01). Although warming did not significantly affect microeukaryotic community structure (ANOSIM: P＞0.05), it enhanced species turnover. Microeukaryotic networks exhibited distinct co-occurrence patterns and topological properties across temperature scenarios. Warming reduced network complexity and stability, as well as altered species interactions. Collectively, these findings are likely to have implications for ecological management of lake ecosystems, in particular semi-arid and arid regions, and for predicting ecological consequences of climate change.

Primer selection impacts the evaluation of microecological patterns in environmental microbiomes

This study revealed that primer selection substantially influences the taxonomic and predicted functional composition and the characterization of microecological patterns, which was not alleviated by close-reference clustering. Biases were relatively consistent across different habitats in community profiling but not in microecological patterns. These primer biases could be attributed to multiple aspects, including taxa specificity, regional hypervariability, and amplification efficiency.