Microbial community assembly and co-occurrence relationship in sediments of the river-dominated estuary and the adjacent shelf in the wet season

Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season

Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe2+ (6.65-17.1 mg/L), NH4+ (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe2+ remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.

The characteristic of compound drought and saltwater intrusion events in the several major river estuaries worldwide

Compound Drought and Saltwater intrusion Events (CDSEs) refer to hydrologic drought and saltwater intrusion occurring simultaneously or consecutively in estuaries, and exacerbate the negative impacts resulting from an individual extreme event. CDSEs have been drawing increasing attention due to their potential adverse impacts on water resources, crop production, and food security. A new Standardized compound Drought and Saltwater intrusion Index (SDSI) was developed in this study to systematically detect changes in the severity of CDSEs in six estuaries (Little Back, Ebro, Rhine, Orange, Pearl River and Murray). The results illustrated that (1) compared to the Standardized Runoff Index (SRI), SDSI effectively characterizes and quantifies the occurrences and severity of CDSEs in major river estuaries worldwide. (2) Temporally, the SDSI trend varied across estuaries. Specifically, a decreasing trend was observed in the Little Back, Ebro, and Orange estuaries, with corresponding Zs values of -2.43, -3.63, and -3.23. (3) Spatially, moderate CDSEs occurred more frequently among different estuaries, and their frequency, duration and severity varied in different estuaries. Notably, Ebro, Rhine and Murray River estuaries had the highest probability of CDSEs, nearing 60%. Among them, the Murray Estuary had the longest average duration, spanning 7.68 months, and the highest severity was 5.94. (4) According to the contributions analysis, saltwater intrusion plays a dominant role in influencing SDSI severity, accounting for a substantial percentage (54%-95.30%) compared to runoff. Notably, the Orange Estuary experienced the greatest impact from saltwater intrusion (81.54%-95.30%), while the Murray Estuary had relatively equal contributions from hydrological drought and saltwater intrusion.

Structure and assembly process of fungal communities in the Yangtze River Estuary

Marine fungi are essential for the ecological function of estuarine ecosystems. However, limited studies have reported on the structure and assembly pattern of the fungal communities in estuaries. The purpose of this study is to reveal the structure and the ecological process of the fungal community in the Yangtze River Estuary (YRE) by using the amplicon sequencing method. Phyla of Ascomycota, Basidiomycota, and Chytridiomycota were dominant in the seawater and sediment samples from YRE. The null model analysis, community-neutral community model (NCM), and phylogenetic normalized stochasticity ratio (pNST) showed that the stochastic process dominated the assembly of fungal communities in YRE. Drift and homogeneous dispersal were the predominant stochastic processes for the fungal community assembly in seawater and sediment samples, respectively. The co-occurrence network analysis showed that fungal communities were more complex and closely connected in the sediment than in the seawater samples. Phyla Ascomycota, Basidiomycota, and Mucoromycota were the potential keystone taxa in the network. These findings demonstrated the importance of stochastic processes for the fungal community assembly, thereby widening our knowledge of the community structure and dynamics of fungi for future study and utilization in the YRE ecosystem.

Role of traveling microplastics as bacterial carriers based on spatial and temporal dynamics of bacterial communities

Microplastics (MPs) are considered as distinct substrates for bacterial colonization, they can carry bacterial communities to travel around environments. The bacterial communities on traveling MPs prefer to be gradually consistent with those on local MPs that were always in the same environment, and this process of change in the bacterial communities on traveling MPs was called 'localization'. However, the dynamics of localization process and their influencing factors are still unclear. Therefore, we simulated the MPs migration process along the water flow direction in the estuary. We used quantitative analysis to study the dynamics of bacterial communities on the migrated MPs. We found the localization characteristics depended on the differences between the former and latter environments, as well as the preexisting bacteria. The localization degree was higher when the former and latter environments were similar. In most cases, compared with the first cultivation of pristine MPs, the time for localization was shorter. Moreover, although the entire bacterial communities tended to be localized, the preexisting bacteria on the migrated MPs had selective effects on subsequent bacterial colonization. Furthermore, the preexisting bacteria on MPs could set up the connections with the bacteria that existed at the latter site, and the stability of the entire bacterial communities on the migrated MPs increased with time. Overall, our findings indicated that the localization characteristics of bacterial communities on traveling MPs were related to the precultured time and environmental differences, which were helpful to understand the colonized bacteria transportation and MPs ecological effects.

Spatio-temporal variation of bacterial community structure in two intertidal sediment types of Jiaozhou Bay

The intertidal sediment environment is dynamic and the biofilm bacterial community within it must constantly adapt, but an understanding of the differences in the biofilm bacterial community within sediments of different types is still relatively limited. The semi-enclosed Jiaozhou Bay has a temperate monsoon climate, with strong currents at the mouth of the bay. In this study, the structure of the bacterial community in Jiaozhou Bay sediment biofilms are described using high-throughput 16 S rRNA gene sequencing and the effects of temporal change and different sediment environment types are discussed. Alpha diversity was significantly higher in sandy samples than in muddy samples. Sandy sediments with increased heterogeneity promote bacterial aggregation. Beta diversity analysis showed significant differences between sediment types and between stations. Proteobacteria and Acidobacteria were significantly more abundant at ZQ, while Campilobacterota was significantly more abundant at LC. The relative abundances of Bacteroidetes, Campilobacterota, Firmicutes, and Chloroflexi were significantly higher in the muddy samples, while Actinobacteria and Proteobacteria were higher in the sandy samples. There were different phylum-level biomarkers between sediment types at different stations. There were also different patterns of functional enrichment in biogeochemical cycles between sediment types and stations with the former having more gene families that differed significantly, highlighting their greater role in determining bacterial function. Bacterial amplicon sequence variant variation between months was less than KEGG ortholog variation between months, presumably the temporal change had an impact on shaping the intertidal sediment bacterial community, although this was less clear at the gene family level. Random forest prediction yielded a combination of 43 family-level features that responded well to temporal change, reflecting the influence of temporal change on sediment biofilm bacteria.

Seasonal dynamics of bacterial community and co-occurrence with eukaryotic phytoplankton in the Pearl River Estuary

In this study, we investigated the taxonomic composition of the bacteria and phytoplankton communities in the Pearl River Estuary (PRE) through Illumina sequencing of the V3-V4 region of the 16 S rRNA gene. Furthermore, their relationships as well as recorded environmental variables were explored by co-occurrence networks. Bacterial community composition was different in two size fractions, as well as along the salinity gradient across two seasons. Free-living (FL) communities were dominated by pico-sized Cyanobacteria (Synechococcus CC9902) while Exiguobacterium, Halomonas and Pseudomonas were predominantly associated with particle-associated (PA) lifestyle, and Cyanobium PCC-6307 exhibited seasonal shifts in lifestyles in different seasons. In wet season, bacterial community composition was characterized by abundance of Cyanobacteria, Actinobacteria, and Bacteroidetes, which were tightly linked with high riverine inflow. While in dry season, Proteobacteria increased in prevalence, especially for Psychrobacter, NOR5/OM60 clade and Pseudomonas, which were thrived in lower water temperature and higher salinity. Moreover, we discovered that differences between PA and FL composition were more significant in the wet season than in the dry season, which may be due to better nutritional conditions of particles (indicated by POC%) in the wet season and then attract more diverse PA populations. Based on the analysis of plastidial 16 S rRNA genes, abundant small-sized mixotrophic phytoplankton (Dinophyceae, Euglenida and Haptophyta) were identified in the PRE. The complexity of co-occurrence network increased from FL to PA fractions in both seasons, which suggested that suspended particles can provide ecological niches for particle-associated colonizers contributing to the maintenance of a more stable community structure. In addition, the majority of phytoplankton species exhibited positive co-occurrences with both other phytoplankton species and bacterial counterparts, indicating the mutual cooperation between phytoplankton assemblages and specific bacterial populations e likely benefited from phytoplankton-derived organic compounds. This study enhances our understanding of the seasonal and spatial dynamics of bacterial communities and their potential relationship with phytoplankton assembly in estuarine waters.

Uncovering the processes of microbial community assembly in the near-surface sediments of a climate-sensitive glacier-fed lake

Glacier-fed lakes are characterized by cold temperatures, high altitudes, and nutrient-poor conditions. Despite these challenging conditions, near-surface sediments of glacier-fed lakes harbor rich microbial communities that are critical for ecosystem functioning and serve as a bridge between aquatic ecology and the deep subsurface biosphere. However, there is limited knowledge regarding the microbial communities and their assembly processes in these sediments, which are highly vulnerable to climate change. To fill this knowledge gap, this study systematically analyzed environmental variables, microbial communities, diversity, co-occurrence relationships, and community assembly processes in the near-surface sediments of a glacier-fed lake in the Tibetan Plateau. The results revealed distinct vertical gradients in microbial diversity and subcommunities, highlighting the significant influence of selection processes and adaptive abilities on microbial communities. Specifically, specialists played a crucial role within the overall microbial communities. Microbial assembly was primarily driven by homogeneous selection, but its influence declined with increasing depth. In contrast, homogenizing dispersal showed an opposite pattern, and the bottom layer exhibited heterogeneous selection and undominated processes. These patterns of microbial assembly were primarily driven by environmental gradients, with significant contributions from processes associated to ammonium and organic matter deposition, as well as chemical precipitation in response to a warming climate. This study enhances our understanding of the microbial communities and assembly processes in the near-surface sediments of glacier-fed lakes and sheds light on geo-microbiological processes in climate-sensitive lacustrine sediments.

Deterministic processes dominate archaeal community assembly from the Pearl River to the northern South China Sea

Archaea play a significant role in the biogeochemical cycling of nutrients in estuaries. However, comprehensive researches about their assembly processes remain notably insufficient. In this study, we systematically examined archaeal community dynamics distinguished between low-salinity and high-salinity groups in water and surface sediments over a 600-kilometer range from the upper Pearl River (PR) to the northern South China Sea (NSCS). Neutral community model analysis together with null model analysis showed that their C-score values were greater than 2, suggesting that deterministic processes could dominate the assembly of those planktonic or benthic archaeal communities at both the low-salinity and high-salinity sites. And deterministic processes contributed more in the low-salinity than high-salinity environments from the PR to the NSCS. Furthermore, through the co-occurrence network analysis, we found that the archaeal communities in the low-salinity groups possessed closer interactions and higher proportions of negative interactions than those in the high-salinity groups, which might be due to the larger environmental heterogeneities reflected by the nutrient concentrations of those low-salinity samples. Collectively, our work systematically investigated the composition and co-occurrence networks of archaeal communities in water as well as sediments from the PR to the NSCS, yielding new insights into the estuary's archaeal community assembly mechanisms.

Effect of Fe3+ on the nutrient removal performance and microbial community in a biofilm system

In this study, the influence of Fe3+ on N removal, microbial assembly, and species interactions in a biofilm system was determined. The results showed that maximum efficiencies of ammonia nitrogen (NH4+-N), total nitrogen (TN), phosphorus (P), and chemical oxygen demand (COD) removal were achieved using 10 mg/L Fe3+, reaching values of 100, 78.85, 100, and 95.8%, respectively, whereas at concentrations of 15 and 30 mg/L Fe3+ suppressed the removal of NH4+-N, TN, and COD. In terms of absolute abundance, the expression of bacterial amoA, narG, nirK, and napA was maximal in the presence of 10 mg/L Fe3+ (9.18 × 105, 8.58 × 108, 1.09 × 108, and 1.07 × 109 copies/g dry weight, respectively). Irrespective of Fe3+ concentrations, the P removal efficiency remained at almost 100%. Candidatus_Competibacter (10.26–23.32%) was identified as the most abundant bacterial genus within the system. Determinism (50%) and stochasticity (50%) contributed equally to microbial community assembly. Co-occurrence network analysis revealed that in the presence of Fe3+, 60.94% of OTUs in the biofilm system exhibited positive interactions, whereas 39.06% exhibited negative interactions. Within the OTU-based co-occurrence network, fourteen species were identified as key microbes. The stability of the system was found to be predominantly shaped by microbial cooperation, complemented by competition for resources or niche incompatibility. The results of this study suggested that during chemical P removal in wastewater treatment plants using biofilm methods, the concentration of supplemental Fe3+ should be maintained at 10 mg/L, which would not only contribute to P elimination, but also enhance N and COD removal.