Effects of different emergent macrophytes on methane flux and rhizosphere microbial communities in wetlands.

Emergent macrophytes are of great importance for the structure and functioning of wetland ecosystems and play a significant role in environmental improvement, element cycling, and greenhouse gas (GHG) emissions. However, our understanding of how GHG fluxes differ among macrophyte species and its links with the microbial communities remain limited. In this study, we investigated the rhizosphere microbial communities (including total bacteria, methanotrophs, and methanogens) and the GHG fluxes associated with four emergent macrophytes-Phragmites australis, Thalia dealbata, Pontederia cordata, and Zizania latifolia-collected from Xuanwu Lake wetland, China. We observed the highest CH4 flux (FCH4) (9.35 ± 2.52 mg·m-2·h-1) from Z. latifolia zone, followed by P. australis, P. cordata, and T. dealbata zones (5.38 ± 1.63, 2.38 ± 2.91, and 2.02 ± 0.69 mg·m-2·h-1, respectively). Methanogenesis was methylotrophic at all sites, as the 13C-CH4 values were higher than -64 ‰ and the fractionation coefficients were lower than 1.055. We found a positive linear relationship between FCH4 and the methanogen community, in particular the relative abundances of Methanobacterium and Methanosarcina, indicating that the variations in FCH4 among the studied macrophyte-dominated zones might be attributed to the differences in rhizosphere microbial communities. The methane emissions in various macrophyte zones might be due to the higher capacity of methanogenesis compared to methane oxidation which was inhibited by nutrient-rich sediments. Our findings provide insights for selecting specific emergent macrophytes characterized by low FCH4 in wetland ecological restoration.

The dual roles of dissimilatory iron reduction in the carbon cycle: The "iron mesh" effect can increase inorganic carbon sequestration.

Dissimilatory iron reduction (DIR) can drive the release of organic carbon (OC) as carbon dioxide (CO2 ) by mediating electron transfer between organic compounds and microbes. However, DIR is also crucial for carbon sequestration, which can affect inorganic-carbon redistribution via iron abiotic-phase transformation. The formation conditions of modern carbonate-bearing iron minerals (ICFe ) and their potential as a CO2 sink are still unclear. A natural environment with modern ICFe , such as karst lake sediment, could be a good analog to explore the regulation of microbial iron reduction and sequential mineral formation. We find that high porosity is conducive to electron transport and dissimilatory iron-reducing bacteria activity, which can increase the iron reduction rate. The iron-rich environment with high calcium and OC can form a large sediment pore structure to support rapid DIR, which is conducive to the formation and growth of ICFe . Our results further demonstrate that the minimum DIR threshold suitable for ICFe formation is 6.65 µmol g-1 dw day-1 . DIR is the dominant pathway (average 66.93%) of organic anaerobic mineralization, and the abiotic-phase transformation of Fe2+ reduces CO2 emissions by ~41.79%. Our findings indicate that as part of the carbon cycle, DIR not only drives mineralization reactions but also traps carbon, increasing the stability of carbon sinks. Considering the wide geographic distribution of DIR and ICFe , our findings suggest that the "iron mesh" effect may become an increasingly important vector of carbon sequestration.

Mechanism of organic phosphorus transformation and its impact on the primary production in a deep oligotrophic plateau lake during stratification.

Global warming is leading to extended stratification in deep lakes, which may exacerbate phosphorus (P) limitation in the upper waters. Conversion of labile dissolved organic P (DOP) is a possible adaptive strategy to maintain primary production. To test this, the spatiotemporal distributions of various soluble P fractions and phosphomonesterase (PME)/phosphodiesterase (PDE) activities were investigated in Lake Fuxian during the stratification period and the transition capacity of organic P and its impact on primary productivity were evaluated. The results indicated that the DOP concentration (mean 0.20 ± 0.05 µmol L-1) was significantly higher than that of dissolved inorganic P (DIP) (mean 0.08 ± 0.03 µmol L-1) in the epilimnion and metalimnion, which were predominantly composed of orthophosphate monoester (monoester-P) and orthophosphate diesters (diester-P). The low ratio of diester-P / monoester-P and high activities of PME and PDE indicate DOP mineralization in the epilimnion and metalimnion. We detected a DIP threshold of approximately 0.19 µmol L-1, corresponding to the highest total PME activity in the lake. Meta-analysis further demonstrated that DIP thresholds of PME activities were prevalent in oligotrophic (0.19 µmol L-1) and mesotrophic (0.74 µmol L-1) inland waters. In contrast to the phosphate-sensitive phosphatase PME, dissolved PDE was expressed independent of phosphate availability and its activity invariably correlated with chlorophyll a, suggesting the involvement of phytoplankton in DOP utilization. This study provides important field evidence for the DOP transformation processes and the strategy for maintaining primary productivity in P-deficient scenarios, which contributes to the understanding of P cycles and the mechanisms of system adaptation to future long-term P limitations in stratified waters.

Epiphytic microorganisms of submerged macrophytes effectively contribute to nitrogen removal.

Submerged macrophytes play important roles in nutrient cycling and are widely used in ecological restoration to alleviate eutrophication and improve water quality in lakes. Epiphytic microbial communities on leaves of submerged macrophytes might promote nitrogen cycling, but the mechanisms and quantification of their contributions remain unclear. Here, four types of field zones with different nutrient levels and submerged macrophytes, eutrophic + Vallisneria natans (EV), eutrophic + V. natans + Hydrilla verticillata, mesotrophic + V. natans + H. verticillata, and eutrophic without macrophytes were selected to investigate the microbial communities that involved in nitrification and denitrification. The alpha diversity of bacterial community was higher in the phyllosphere than in the water, and that of H. verticillata was higher compared to V. natans. Bacterial community structures differed significantly between the four zones. The highest relative abundance of dominant bacterioplankton genera involved in nitrification and denitrification was observed in the EV zone. Similarly, the alpha diversity of the epiphytic ammonia-oxidizing archaea and nosZI-type denitrifiers were highest in the EV zone. Consist with the diversity patterns, the potential denitrification rates were higher in the phyllosphere than those in the water. Higher potential denitrification rates in the phyllosphere were also found in H. verticillata than those in V. natans. Anammox was not detected in all samples. Nutrient loads, especially nitrogen concentrations were important factors influencing potential nitrification, denitrification rates, and bacterial communities, especially for the epiphytic nosZI-type taxa. Overall, we observed that the phyllosphere harbors more microbes and promotes higher denitrification rates compared to water, and epiphytic bacterial communities are shaped by nitrogen nutrients and macrophyte species, indicating that epiphytic microorganisms of submerged macrophytes can effectively contribute to the N removal in shallow lakes.

Methane ebullition fluxes and temperature sensitivity in a shallow lake.

Inland waters are important sources of atmospheric methane (CH4), with a major contribution from the CH4 ebullition pathway. However, there is still a lack of CH4 ebullition flux (eFCH4) and their temperature sensitivity (Q10) in shallow lakes, which might lead to large uncertainties in CH4 emission response from aquatic to climate and environmental change. Herein, the magnitude and regulatory of two CH4 pathways (ebullition and diffusion) were studied in subtropical Lake Chaohu, China, using the real-time portable greenhouse gas (GHG) analyzer-floating chamber method at 18 sites over four seasons. eFCH4 (12.06 ± 4.10 nmol m-2 s-1) was the dominant contributing pathway (73.0 %) to the two CH4 emission pathways in Lake Chaohu. The whole-lake mass balance calculation demonstrated that 56.6 % of the CH4 emitted from the sediment escaped through the ebullition pathway. eFCH4 was significantly higher in the western (WL: 16.54 ± 22.22 nmol m-2 s-1) and eastern lake zones (EL: 11.89 ± 15.43 nmol m-2 s-1) than in the middle lake zone (ML: 8.86 ± 13.78 nmol m-2 s-1; p < 0.05) and were significantly higher in the nearshore lake zone (NL: 15.94 ± 19.58 nmol m-2 s-1) than in the pelagic lake zone (PL: 6.64 ± 12.37 nmol m-2 s-1; p < 0.05). eFCH4 was significantly higher in summer (32.12 ± 13.82 nmol m-2 s-1) than in other seasons (p < 0.05). eFCH4 had a strong temperature dependence. Sediment total organic carbon (STOC) is an important ecosystem level Q10 driver of eFCH4. The meta-analysis also verified that across ecosystems the ecosystem-level Q10 of eFCH4 was significantly positively correlated with STOC and latitude (p < 0.05). This study suggests that eFCH4 will become increasingly crucial in shallow lake ecosystems as climate change and human activities increase. The potential increase in ebullition fluxes in high-latitude lakes is of great importance.

Diffusion kinetic processes and release risks of trace metals in plateau lacustrine sediments.

The ecological risk posed by trace metals in the plateau lacustrine sediments of China has attracted worldwide attentions. A better understanding of the kinetic diffusion processes and bioavailability of these metals in plateau lakes is needed. Using the diffusive gradient in thin films (DGT) and Rhizon, concentrations of Mn, Mo, Ni, Cr, and Co in the sediments, labile fractions, and interstitial water of Lake Fuxian were comprehensively analyzed. According to the DGT-induced fluxes in sediments (DIFS) model, fully sustained and unsustained resupplies are possible ways in which metals are released from solids to the solution. Moreover, the resupply characteristics of metals varied at different depths in the sediments and at different sites in the lake. Based on the DIFS model, the effective concentrations (CE) of the trace metals were calculated and all except Cr showed good linear relationships with the DGT-labile concentrations, indicating that the CE values were valuable for predicting metal bioavailability. According to the CE values, the metal contamination released from the sediments was relatively low based on the Monte Carlo simulation. This study provides a comprehensive solution for studying the environmental behavior and potential ecological risks of toxic metals in sedimentary environment.

Microcystis blooms caused the decreasing richness of and interactions between free-living microbial functional genes in Lake Taihu, China.

Microcystis blooms have a marked effect on microbial taxonomical diversity in eutrophic lakes, but their influence on the composition of microbial functional genes is still unclear. In this study, the free-living microbial functional genes (FMFG) composition was investigated in the period before Microcystis blooms (March) and during Microcystis blooms (July) using a comprehensive functional gene array (GeoChip 5.0). The composition and richness of FMFG in the water column was significantly different between these two periods. The FMFG in March was enriched in the functional categories of nitrogen, sulfur, and phosphorus cycling, whereas the FMFG in July was enriched in carbon cycling, organic remediation, and metal homeostasis. Molecular ecological network analysis further demonstrated fewer functional gene interactions and reduced complexity in July than in March. Module hubs of the March network were mediated by functional genes associated with carbon, nitrogen, sulfur, and phosphorus, whereas those in July by a metal homeostasis functional gene. We also observed stronger deterministic processes in the FMFG assembly in July than in March. Collectively, this study demonstrated that Microcystis blooms induced significant changes in FMFG composition and metabolic potential, and abundance-information, which can support the understanding and management of biogeochemical cycling in eutrophic lake ecosystems.

Greater transmission capacities and small-world characteristics of bacterial communities in the above- than those in the below- ground niches of a typical submerged macrophyte, Vallisneria natans.

Leaves and roots of submerged macrophytes provide extended surfaces and stable internal tissues for distinct microorganisms to rest, but how these microorganisms interact with each other across different niches and ultimately drive the distribution through horizontal and vertical transmissions remains largely undetermined. Knowledge of the mechanisms of assemblage and transmission in aquatic macrophytes-associated microbial communities will help to better understanding their important roles in plant fitness and benefit ecological functions. Here, we conducted a microcosmic experiment based on in situ lake samples to investigate the bacterial community assemblage, transmission, and co-occurrence patterns in different niches of a typical submerged macrophyte, Vallisneria natans (V. natans), including seed endosphere, as well as environmental (water and bulk sediment), epiphytic (phyllosphere and rhizosphere), and endophytic (leaf and root endosphere) microhabitats of both leaves and roots representatives of the above- and below- ground niches (AGNs and BGNs), respectively. We found the bacterial communities colonized in epiphytic niches not only exhibited the highest diversity compared to adjacent environmental and endophytic niches, but also dominated the interactions between those bacterial members of neighboring niches in both AGNs and BGNs. The host plants promoted niche specificity at bacterial community-level, as confirmed by the proportion of bacterial specialists increased with plant proximity, especially in the BGNs. Furthermore, the bacterial taxa colonized in the AGNs exhibited higher horizontal and vertical transmission capacities than those in the BGNs, especially in the vertical transmission from seeds to leaves (41.38 %) than roots (0.42 %). Meanwhile, the bacterial co-occurrence network in AGNs was shown to have stronger small-world characteristics but weaker stability than those in the BGNs. Overall, this study cast new light on the plant microbiome in the aquatic environment, thus better promoting the potential development of strategies for breeding aquatic macrophyte holobiont with enhanced water purification and pollutant removal capabilities in the future.

Habitat-specific regulation of bacterial community dynamics during phytoplankton bloom succession in a subtropical eutrophic lake.

Phytoplankton blooms, an important indicator of severe eutrophication, are a globally significant consequence of anthropogenic activities and climate change on freshwater lakes. Shifts in microbial communities during phytoplankton blooms have been extensively investigated, yet we have a limited understanding of how distinct assembly processes underlying the temporal dynamics of freshwater bacterial communities within different habitats respond to the succession of phytoplankton blooms. To address this knowledge gap, we collected both water and sediment samples in a subtropical eutrophic lake over a complete period of phytoplankton blooms to assess the dynamics of bacterial communities and the temporal shifts in assembly processes. Our results showed that phytoplankton blooms strongly altered the diversity, composition, and coexistence patterns of both planktonic and sediment bacterial communities (PBC and SBC), but the successional patterns differed between PBC and SBC. PBC were less temporally stable under bloom-induce disturbances, with higher variations in temporal dynamics and greater sensitivity to environmental fluctuations. Furthermore, the temporal assembly patterns of bacterial communities in both habitats were mainly driven by homogeneous selection and ecological drift. In the PBC, the role of selection decreased over time, while ecological drift became increasingly important. Conversely, in the SBC, the relative impact of selection and ecological drift on community assemblages fluctuated less over time, with selection remaining the dominant process throughout the bloom.

Hydrogenotrophic pathway dominates methanogenesis along the river-estuary continuum of the Yangtze River.

Rivers are considered as an important source of methane (CH4) to the atmosphere, but our understanding for the methanogenic pathway in rivers and its linkage with CH4 emission is very limited. Here, we investigated the diffusive flux of CH4 and its stable carbon isotope signature (δ13C-CH4) along the river-estuary continuum of the Yangtze River. The diffusive CH4 flux was estimated to 27.9 ± 11.4 µmol/m2/d and 36.5 ± 24.4 µmol/m2/d in wet season and dry season, respectively. The δ13C-CH4 values were generally lower than -60‰, with the fractionation factor (αc) higher than 1.055 and the isotope separation factor (εc) ranged from 55 to 100. In situ microbial composition showed that hydrogenotrophic methanogens accounts for over 70% of the total reads. Moreover, the incubation test showed that the headspace CH4 concentration by adding CO2/H2 to the sediment was orders of magnitude higher than that by adding trimethylamine and sodium acetate. These results jointly verified the river-estuary continuum is a minor CH4 source and dominated by hydrogenotrophic pathway. Based on the methanogenic pathway here and previous reported data in the same region, the historical variation of diffusive CH4 flux was calculated and results showed that CH4 emission has reduced 82.5% since the construction of Three Gorges Dam (TGD). Our study verified the dominant methanogenic pathway in river ecosystems and clarified the effect and mechanism of dam construction on riverine CH4 emission.

Microbial Diversity Biased Estimation Caused by Intragenomic Heterogeneity and Interspecific Conservation of 16S rRNA Genes.

The 16S rRNA gene has been extensively used as a molecular marker to explore evolutionary relationships and profile microbial composition throughout various environments. Despite its convenience and prevalence, limitations are inevitable. Variable copy numbers, intragenomic heterogeneity, and low taxonomic resolution have caused biases in estimating microbial diversity. Here, analysis of 24,248 complete prokaryotic genomes indicated that the 16S rRNA gene copy number ranged from 1 to 37 in bacteria and 1 to 5 in archaea, and intragenomic heterogeneity was observed in 60% of prokaryotic genomes, most of which were below 1%. The overestimation of microbial diversity caused by intragenomic variation and the underestimation introduced by interspecific conservation were calculated when using full-length or partial 16S rRNA genes. Results showed that, at the 100% threshold, microbial diversity could be overestimated by as much as 156.5% when using the full-length gene. The V4 to V5 region-based analyses introduced the lowest overestimation rate (4.4%) but exhibited slightly lower species resolution than other variable regions under the 97% threshold. For different variable regions, appropriate thresholds rather than the canonical value 97% were proposed for minimizing the risk of splitting a single genome into multiple clusters and lumping together different species into the same cluster. This study has not only updated the 16S rRNA gene copy number and intragenomic variation information for the currently available prokaryotic genomes, but also elucidated the biases in estimating prokaryotic diversity with quantitative data, providing references for choosing amplified regions and clustering thresholds in microbial community surveys. IMPORTANCE Microbial diversity is typically analyzed using marker gene-based methods, of which 16S rRNA gene sequencing is the most widely used approach. However, obtaining an accurate estimation of microbial diversity remains a challenge, due to the intragenomic variation and low taxonomic resolution of 16S rRNA genes. Comprehensive examination of the bias in estimating such prokaryotic diversity using 16S rRNA genes within ever-increasing prokaryotic genomes highlights the importance of the choice of sequencing regions and clustering thresholds based on the specific research objectives.

The Effects of Intraguild Predation on Phytoplankton Assemblage Composition and Diversity: A Mesocosm Experiment.

Intraguild predation (IGP) can have a significant impact on phytoplankton biomass, but its effects on their diversity and assemblage composition are not well understood. In this study, we constructed an IGP model based on the common three-trophic food chain of "fish (or shrimp)-large branchiopods (Daphnia)-phytoplankton", and investigated the effects of IGP on phytoplankton assemblage composition and diversity in outdoor mesocosms using environmental DNA high-throughput sequencing. Our results indicated that the alpha diversities (number of amplicon sequence variants and Faith's phylogenetic diversity) of phytoplankton and the relative abundance of Chlorophyceae increased with the addition of Pelteobagrus fulvidraco, while similar trends were found in alpha diversities but with a decrease in the relative abundance of Chlorophyceae in the Exopalaemon modestus treatment. When both predators were added to the community, the strength of collective cascading effects on phytoplankton alpha diversities and assemblage composition were weaker than the sum of the individual predator effects. Network analysis further showed that this IGP effect also decreased the strength of collective cascading effects in reducing the complexity and stability of the phytoplankton assemblages. These findings contribute to a better understanding of the mechanisms underlying the impacts of IGP on lake biodiversity, and provide further knowledge relevant to lake management and conservation.

Biogeographical and Biodiversity Patterns of Marine Planktonic Bacteria Spanning from the South China Sea across the Gulf of Bengal to the Northern Arabian Sea.

Understanding the biogeographical and biodiversity patterns of bacterial communities is essential in unraveling their responses to future environmental changes. However, the relationships between marine planktonic bacterial biodiversity and seawater chlorophyll a are largely understudied. Here, we used high-throughput sequencing to study the biodiversity patterns of marine planktonic bacteria across a broad chlorophyll a gradient spanning from the South China Sea across the Gulf of Bengal to the northern Arabian Sea. We found that the biogeographical patterns of marine planktonic bacteria complied with the scenario of homogeneous selection, with chlorophyll a concentration being the key environmental selecting variable of bacteria taxa. The relative abundance of Prochlorococcus, the SAR11 clade, the SAR116 clade, and the SAR86 clade significantly decreased in habitats with high chlorophyll a concentrations (>0.5 µg/L). Free-living bacteria (FLB) and particle-associated bacteria (PAB) displayed contrasting alpha diversity and chlorophyll a relationships with a positive linear correlation for FLB but a negative correlation for PAB. We further found that PAB had a narrower niche breadth of chlorophyll a than did FLB, with far fewer bacterial taxa being favored at higher chlorophyll a concentrations. Higher chlorophyll a concentrations were linked to the enhanced stochastic drift and reduced beta diversity of PAB but to the weakened homogeneous selection, enhanced dispersal limitation, and increased beta diversity of FLB. Taken together, our findings might broaden our knowledge about the biogeography of marine planktonic bacteria and advance the understanding of bacterial roles in predicting ecosystem functioning under future environmental changes that are derived from eutrophication. IMPORTANCE One of the long-standing interests of biogeography is to explore diversity patterns and uncover their underlying mechanisms. Despite intensive studies on the responses of eukaryotic communities to chlorophyll a concentrations, we know little about how changes in seawater chlorophyll a concentrations affect free-living bacteria (FLB) and particle-associated bacteria (PAB) diversity patterns in natural systems. Our biogeography study demonstrated that marine FLB and PAB displayed contrasting diversity and chlorophyll a relationships and exhibited completely different assembly mechanisms. Our findings broaden our knowledge about the biogeographical and biodiversity patterns of marine planktonic bacteria in nature systems and suggest that PAB and FLB should be considered independently in predicting marine ecosystem functioning under future frequent eutrophication.

Unexpected enrichment of antibiotic resistance genes and organic remediation genes in high-altitude lakes at Eastern Tibetan Plateau.

Elevation has a strong effect on aquatic microbiome. However, we know little about the effects of elevation on functional genes, especially antibiotic resistance genes (ARGs) and organic remediation genes (ORGs) in freshwater ecosystems. In this study, we analyzed five classes of functional genes including ARGs, metal resistance genes (MRGs), ORGs, bacteriophages, and virulence genes between two high-altitude lakes (HALs) and two low-altitude lakes (LALs) in Mountain Siguniang at Eastern Tibetan Plateau by means of GeoChip 5.0. No differences (Student's t-test, p > 0.05) of gene richness including ARGs, MRGs, ORGs, bacteriophages, and virulence genes in HALs and LALs were found. The abundance of most ARGs and ORGs was higher in HALs than in LALs. For MRGs, the abundance of macro metal resistance genes of potassium, calcium, and aluminum was higher in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d > 0.8). The abundance of some heavy metal resistance genes of lead and mercury was lower in HALs than in LALs (Student's t-test, p < 0.05; all Cohen's d < -0.8). The composition of these functional genes in HALs differed significantly from in LALs. The functional gene network in HALs was also more complex than that in LALs. We speculate that enrichment of ARGs and ORGs in HALs is related to different microbial communities, exogenous ARGs, and enriched persistent organic pollutants through long-range atmospheric transport driven by the Indian monsoon. This study highlights the unexpected enrichment of ARGs, MRGs, and ORGs in remote lakes at high elevations.

Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments.

Conventional aerobic CH4-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O2 gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH4 with the help of riboflavin when O2 was unavailable. Within the MOB consortium, MOB transformed CH4 to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH4 oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH4 emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH4 sink in iron-rich sediments.

Co-occurrence pattern of bacteria and fungi on the leaves of the invasive aquatic plant Alternanthera philoxeroides.

The microbes that are attached to aquatic plants play critical roles in nutrient cycles and the maintenance of water quality. However, their community compositions, biodiversity and functions have not been well explored for the invasive plants in inland waters. Here, the co-occurrence patterns between bacteria and fungi on the leaves of Alternanthera philoxeroides and their potential ecological interactions were studied during the growing seasons. Along with significant variations in the alpha diversity of attached microbes over time, shifts in their community composition were significantly associated with the dynamics of plant stoichiometry, substrate composition and extracellular enzyme activity. Deterministic processes (heterogenous selection) play a predominant role in community assembly of the attached bacteria, while stochasticity (undominated process) was the major driver for the attached fungal assembly. Compared with the free-living microbial network, the attached microbial network was structurally simple but highly modular. The attached microbes had more intra-phylum links (primarily within the phyla Actinomycetota, Alphaproteobacteria, Bacillota and Basidiomycota) and distinct co-exclusion patterns between bacteria and fungi in the modules. In summary, the study will be helpful in understanding the microbes and their interactions in the phyllosphere of A. philoxeroides, an key invasive species under national management and control.

Evaluating potential ecological risks of emerging toxic elements in lacustrine sediments: A case study in Lake Fuxian, China.

The fragile ecosystems of plateau lakes are in face of ecological risks from emerging toxic elements. Beryllium (Be) and thallium (Tl) have been considered priority control metals in recent years owing to their persistence, toxicity, and bioaccumulation. However, the toxic factors of Be and Tl are scarce and ecological risks of them in the aquatic environment were seldom investigated. Hence, this study developed a framework for calculating the potential ecological risk index (PERI) of Be and Tl in aquatic systems and used it to assess the ecological risks of Be and Tl in Lake Fuxian, a plateau lake in China. The toxicity factors of Be and Tl were calculated to be 40 and 5, respectively. In sediments of Lake Fuxian, the concentrations of Be and Tl were between 2.18 and 4.04 mg/kg and 0.72-0.94 mg/kg, respectively. The spatial distribution indicated that Be was more abundant in the eastern and southern regions, and Tl had higher concentrations near the northern and southern banks, consistent with the distribution of anthropogenic activities. The background values were calculated as 3.38 mg/kg and 0.89 mg/kg for Be and Tl, respectively. In comparison with Be, Tl was more enriched in Lake Fuxian. The increasing Tl enrichment has been attributed to anthropogenic activities (e.g., coal burning and non-ferrous metal production), especially since the 1980s. Generally, Be and Tl contamination has decreased over the past several decades, from moderate to low, since the 1980s. The ecological risk of Tl was low, whereas Be might have caused low to moderate ecological risks. In the future, the obtained toxic factors of Be and Tl in this study can be adopted in assessing the ecological risks of them in sediments. Moreover, the framework can be employed for the ecological risk assessment of other newly emerging toxic elements in the aquatic environment.

Lower Compositional Variation and Higher Network Complexity of Rhizosphere Bacterial Community in Constructed Wetland Compared to Natural Wetland.

Macrophyte rhizosphere microbes, as crucial components of the wetland ecosystem, play an important role in maintaining the function and stability of natural and constructed wetlands. Distinct environmental conditions and management practices between natural and constructed wetlands would affect macrophytes rhizosphere microbial communities and their associated functions. Nevertheless, the understanding of the diversity, composition, and co-occurrence patterns of the rhizosphere bacterial communities in natural and constructed wetlands remains unclear. Here, we used 16S rRNA gene high-throughput sequencing to characterize the bacterial community of the rhizosphere and bulk sediments of macrophyte Phragmites australis in representative natural and constructed wetlands. We observed higher alpha diversity of the bacterial community in the constructed wetland than that of the natural wetland. Additionally, the similarity of bacterial community composition between rhizosphere and bulk sediments in the constructed wetland was increased compared to that of the natural wetland. We also found that plants recruit specific taxa with adaptive functions in the rhizosphere of different wetland types. Rhizosphere samples of the natural wetland significantly enriched the functional bacterial groups that mainly related to nutrient cycling and plant-growth-promoting, while those of the constructed wetland-enriched bacterial taxa with potentials for biodegradation. Co-occurrence network analysis showed that the interactions among rhizosphere bacterial taxa in the constructed wetland were more complex than those of the natural wetland. This study broadens our understanding of the distinct selection processes of the macrophytes rhizosphere-associated microbes and the co-occurrence network patterns in different wetland types. Furthermore, our findings emphasize the importance of plant-microbe interactions in wetlands and further suggest P. australis rhizosphere enriched diverse functional bacteria that might enhance the wetland performance through biodegradation, nutrient cycling, and supporting plant growth.

Habitats modulate influencing factors shaping the spatial distribution of bacterial communities along a Tibetan Plateau riverine wetland.

The Tibetan Plateau riverine wetland is very sensitive to global climate change. Understanding the mechanisms that maintain the spatial patterns of bacterial communities provides insight into the dominant biogeochemical processes within the plateau riverine wetlands. Nonetheless, the spatial distribution of bacterial communities along these wetlands has rarely been explored. We investigated the spatial patterns of bacterial community within rhizosphere soil, bulk soil, and sediment samples collected along the Yarlung Tsangpo riverine wetland (YTRW), the longest plateau riverine wetland in China. Our results indicated that the diversity of bacterial communities in all three habitats increased significantly along the YTRW. The slope of the linear relationship between distance and bacterial community diversity in sediment was steeper than those for bulk and rhizosphere soils. Furthermore, bacterial communities in all three habitats showed significant distance-decay relationships. A combination of historical factors (geographical distance and climatic factors) and contemporary environmental heterogeneity (edaphic properties) controlled spatial distributions of bacterial communities in all three habitats, although climatic factors were predominant. Climatic factors affected rhizosphere bacterial communities more than those in bulk soil and sediment. Co-occurrence network analysis revealed that the potential interactions between bacterial taxa may decrease along the YTRW. This field investigation highlighted that the climatic factors strongly influenced the spatial distribution of bacterial communities along the YTRW; however, habitat differences among rhizosphere soil, bulk soil, and sediment samples affected the relative importance of climatic factors on spatial distributions of the associated bacterial communities. These findings would improve the understanding of biogeochemical processes in these typical habitats and potential alterations provoked by climate change.

Improved Assembly of Metagenome-Assembled Genomes and Viruses in Tibetan Saline Lake Sediment by HiFi Metagenomic Sequencing.

With the development and reduced costs of high-throughput sequencing technology, environmental dark matter, such as novel metagenome-assembled genomes (MAGs) and viruses, is now being discovered easily. However, due to read length limitations, MAGs and viromes often suffer from genome discontinuity and deficiencies in key functional elements. Here, by applying long-read sequencing technology to sediment samples from a Tibetan saline lake, we comprehensively analyzed the performance of high-fidelity (HiFi) reads and the possibility of integration with short-read next-generation sequencing (NGS) data. In total, 207 full-length nonredundant 16S rRNA gene sequences and 19 full-length nonredundant 18S rRNA genes were directly obtained from HiFi reads, which greatly surpassed the retrieval performance of NGS technology. We carried out a cross-sectional comparison among multiple assembly strategies, referred to as 'NGS', 'Hybrid (NGS+HiFi)', and 'HiFi'. Two MAGs and 29 viruses with circular genomes were reconstructed using HiFi reads alone, indicating the great power of the 'HiFi' approach to assemble high-quality microbial genomes. Among the 3 strategies, the 'Hybrid' approach produced the highest number of medium/high-quality MAGs and viral genomes, while the ratio of MAGs containing 16S rRNA genes was significantly improved in the 'HiFi' assembly results. Overall, our study provides a practical metagenomic resolution for analyzing complex environmental samples by taking advantage of both the short-read and HiFi long-read sequencing methods to extract the maximum amount of information, including data on prokaryotes, eukaryotes, and viruses, via the 'Hybrid' approach. IMPORTANCE To expand the understanding of microbial dark matter in the environment, we did the first comparative evaluation of multiple assembly strategies based on high-throughput short-read and HiFi data from lake sediments metagenomic sequencing. The results demonstrated great improvement of the 'Hybrid' assembly method (short-read next-generation sequencing data plus HiFi data) in the recovery of medium/high-quality MAGs and viral genomes. Further analysis showed that HiFi data is important to retrieve the complete circular prokaryotic and viral genomes. Meanwhile, hundreds of full-length 16S/18S rRNA genes were assembled directly from HiFi data, which facilitated the species composition studies of complex environmental samples, especially for understanding micro-eukaryotes. Therefore, the application of the latest HiFi long-read sequencing could greatly improve the metagenomic assembly integrity and promote environmental microbiome research.