Co-occurrence of planktonic bacteria and archaea affects their biogeographic patterns in China's coastal wetlands

Spatiotemporal Variations in Co-Occurrence Patterns of Planktonic Prokaryotic Microorganisms along the Yangtze River

Bacteria and archaea are foundational life forms on Earth and play crucial roles in the development of our planet's biological hierarchy. Their interactions influence various aspects of life, including eukaryotic cell biology, molecular biology, and ecological dynamics. However, the coexistence network patterns of these microorganisms within natural river ecosystems, vital for nutrient cycling and environmental health, are not well understood. To address this knowledge gap, we systematically explored the non-random coexistence patterns of planktonic bacteria and archaea in the 6000-km stretch of the Yangtze River by using high-throughput sequencing technology. By analyzing the O/R ratio, representing the divergence between observed (O%) and random (R%) co-existence incidences, and the module composition, we found a preference of both bacteria and archaea for intradomain associations over interdomain associations. Seasons notably influenced the co-existence of bacteria and archaea, and archaea played a more crucial role in spring as evidenced by their predominant presence of interphyla co-existence and more species as keystone ones. The autumn network was characterized by a higher node or edge number, greater graph density, node degree, degree centralization, and nearest neighbor degree, indicating a more complex and interconnected structure. Landforms markedly affected microbial associations, with more complex networks and more core species found in plain and non-source areas. Distance-decay analysis suggested the importance of geographical distance in shaping bacteria and archaea co-existence patterns (more pronounced in spring). Natural, nutrient, and metal factors, including water temperature, NH4+-N, Fe, Al, and Ni were identified as crucial determinants shaping the co-occurrence patterns. Overall, these findings revealed the dynamics of prokaryotic taxa coexistence patterns in response to varying environmental conditions and further contributed to a broader understanding of microbial ecology in freshwater biogeochemical cycling.

The diversity of planktonic bacteria driven by environmental factors in different mariculture areas in the East China Sea

Planktonic bacteria play a crucial role in sustaining the ecological balance of aquatic ecosystems. However, their seasonal variations in different aquaculture areas within the East China Sea, along with their correlation to environmental factors, have not been extensively explored. In this study, each area with 3 sample points were set up to represent the fish aquaculture area, shellfish aquaculture area and non-aquaculture area. In 2019, we undertook four marine surveys along the Xiasanhengshan uninhabited island, during which we gathered surface seawater samples for both physicochemical analysis and high-throughput sequencing. This allowed us to obtain data about the physicochemical properties and microbial composition in each surveyed region. A short-term eutrophication phenomenon was present in the sea, and the spatial and temporal distribution of planktonic bacteria differed based on the mariculture area. At the phylum level, Proteobacteria accounted for >50 % of the community abundance in winter, spring, and autumn, while Cyanobacteria accounted for >30 % of the community abundance in summer. Because Cyanobacteria blooms are likely in summer, the relationship between Cyanobacteria and environmental factors was studied. Redundancy analysis showed that Cyanobacteria were consistently positively correlated with phosphate. Eutrophication and abnormal proliferation of Cyanobacteria in the study area necessitate ameliorations in the mariculture structure. The variation of genus in Proteobacteria is consistent with that of eutrophication, so some genera in Proteobacteria have the potential to become biological indicator species.

Effects of an efficient straw decomposition system mediated by Stropharia rugosoannulata on soil properties and microbial communities in forestland

Cultivation of Stropharia rugosoannulata with straw in forestland is effective for straw biodegradation and can prevent the waste of straw resources and environmental pollution and generate economic benefits. However, there is a lack of systematic evaluation of spent mushroom substrate (SMS) input into forestland, such as soil properties and microbial succession. In this experiment, 0 (CK), 10 (SA), 20 (SB), 30 (SC), 40 (SD), and 50 (SE) kg/m2 straw were used to cultivate S. rugosoannulata, and two soil layers (0-10 cm, 10-20 cm) of the cultivated forestland were analyzed. The results indicated that SMS significantly promoted nutrient accumulation in forestland. The bacterial alpha diversity in the SC treatment group was greater than that in the control and gradually decreased to the control level with interannual changes, while the trend of fungal alpha diversity was opposite to that of bacterial alpha diversity. Furthermore, the SC treatment group positively affected soil nitrogen metabolism-related microorganisms for two consecutive years and significantly promoted tree growth. Habitat niche breadth and null model analysis revealed that bacterial communities were more sensitive than fungal communities after SMS input. Linear mixed model (LMM) analysis revealed that SMS supplementation significantly positively affected bacteria (Gammaproteobacteria and Bacteroidota) and significantly negatively affected fungi (Coniochaetales). The constructed fungal-bacterial co-occurrence networks exhibited modularity, and the five types of bacteria were significantly correlated with soil organic matter (SOM), soil organic carbon (SOC), available potassium (AK), available phosphorus (AAP) and available nitrogen (AN) levels. The structural equation model (SEM) showed that bacterial diversity responded more to changes in soil nutrients than did fungal diversity. Overall, 30 kg/m2 of straw decomposition and 2 years of continuous cultivation were beneficial to soil health. This study provides new insights into the rational decomposition of straw and maintenance of forestland ecological balance by S. rugosoannulata.

Stepwise degradation of organic matters driven by microbial interactions in China΄s coastal wetlands: Evidence from carbon isotope analysis

The microbial "unseen majority" as drivers of carbon cycle represent a significant source of uncertain climate change. To comprehend the resilience of life forms on Earth to climate change, it is crucial to incorporate knowledge of intricate microbial interactions and their impact to carbon transformation. Combined with carbon stable isotope analysis and high-throughput sequencing technology, the underlying mechanism of microbial interactions for organic carbon degradation has been elucidated. Niche differentiation enabled archaea to coexist with bacteria mainly in a cooperative manner. Bacteria composed of specialists preferred to degrade lighter carbon, while archaea were capable of utilizing heavier carbon. Microbial resource-dependent interactions drove stepwise degradation of organic matter. Bacterial cooperation directly facilitated the degradation of algae-dominated particulate organic carbon, while competitive feeding of archaea caused by resource scarcity significantly promoted the mineralization of heavier particulate organic carbon and then the release of dissolved inorganic carbon. Meanwhile, archaea functioned as a primary decomposer and collaborated with bacteria in the gradual degradation of dissolved organic carbon. This study emphasized microbial interactions driving carbon cycle and provided new perspectives for incorporating microorganisms into carbon biogeochemical models.

Effects of Cascade Reservoirs on Spatiotemporal Dynamics of the Sedimentary Bacterial Community: Co-occurrence Patterns, Assembly Mechanisms, and Potential Functions

Dam construction as an important anthropogenic activity significantly influences ecological processes in altered freshwater bodies. However, the effects of multiple cascade dams on microbial communities have been largely overlooked. In this study, the spatiotemporal distribution, co-occurrence relationships, assembly mechanisms, and functional profiles of sedimentary bacterial communities were systematically investigated in 12 cascade reservoirs across two typical karst basins in southwest China over four seasons. A significant spatiotemporal heterogeneity was observed in bacterial abundance and diversity. Co-occurrence patterns in the Wujiang Basin exhibited greater edge counts, graph density, average degree, robustness, and reduced modularity, suggesting more intimate and stronger ecological interactions among species than in the Pearl River Basin. Furthermore, Armatimonadota and Desulfobacterota, identified as keystone species, occupied a more prominent niche than the dominant species. A notable distance-decay relationship between geographical distance and community dissimilarities was identified in the Pearl River Basin. Importantly, in the Wujiang Basin, water temperature emerged as the primary seasonal variable steering the deterministic process of bacterial communities, whereas 58.5% of the explained community variance in the neutral community model (NCM) indicated that stochastic processes governed community assembly in the Pearl River Basin. Additionally, principal component analysis (PCA) revealed more pronounced seasonal dynamics in nitrogen functional compositions than spatial variation in the Wujiang Basin. Redundancy analysis (RDA) results indicated that in the Wujiang Basin, environmental factors and in Pearl River Basin, geographical distance, reservoir age, and hydraulic retention time (HRT), respectively, influenced the abundance of nitrogen-related genes. Notably, these findings offer novel insights: building multiple cascade reservoirs could lead to a cascading decrease in biodiversity and resilience in the river-reservoir ecosystem.

K. Habeebullah S, Ali AK, Al-Zakri WM. Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf

Kuwaiti territorial waters of the northwest Arabian Gulf represent a unique aquatic ecosystem prone to various environmental and anthropogenic stressors that pose significant constraints on the resident biota which must withstand extreme temperatures, salinity levels, and reducing conditions, among other factors to survive. Such conditions create the ideal environment for investigations into novel functional genetic adaptations of resident organisms. Firstly, however, it is essential to identify said organisms and understand the dynamic nature of their existence. Thus, this study provides the first comprehensive analysis of bacterial and archaeal community structures in the unique waters of Kuwait located in the Northwest Arabian Gulf and analyzes their variations with respect to depth, season, and location, as well as their susceptibility to changes in abundance with respect to various physicochemical parameters. Importantly, this study is the first of its kind to utilize a shotgun metagenomics approach with sequencing performed at an average depth of 15 million paired end reads per sample, which allows for species-level community profiling and sets the framework for future functional genomic investigations. Results showed an approximately even abundance of both archaeal (42.9%) and bacterial (57.1%) communities, but significantly greater diversity among the bacterial population, which predominantly consisted of members of the Proteobacteria, Cyanobacteria, and Bacteroidetes phyla in decreasing order of abundance. Little to no significant variations as assessed by various metrics including alpha and beta diversity analyses were observed in the abundance of archaeal and bacterial populations with respect to depth down the water column. Furthermore, although variations in differential abundance of key genera were detected at each of the three sampling locations, measurements of species richness and evenness revealed negligible variation (ANOVA p<0.05) and only a moderately defined community structure (ANOSIM r2 = 0.243; p>0.001) between the various locations. Interestingly, abundance of archaeal community members showed a significant increase (log2 median ratio of RA = 2.6) while the bacterial population showed a significant decrease (log2 median ratio = -1.29) in the winter season. These findings were supported by alpha and beta diversity analyses as well (ANOSIM r2 = 0.253; p>0.01). Overall, this study provides the first in-depth analysis of both bacterial and archaeal community structures developed using a shotgun metagenomic approach in the waters of the Northwest Arabian Gulf thus providing a framework for future investigations of functional genetic adaptations developed by resident biota attempting to survive in the uniquely extreme conditions to which they are exposed.

Tidal dynamics regulates potential coupling of carbon‑nitrogen‑sulfur cycling microbes in intertidal flats

Tide-driven hydrodynamic process causes significant geochemical gradients that influence biogeochemical cycling and ecological functioning of estuarine and coastal ecosystems. However, the effects of tidal dynamics on microbial communities, particularly at the functional gene level, remain unclear even though microorganisms play critical roles in biogeochemical carbon (C), nitrogen (N) and sulfur (S) cycling. Here, we used 16S rRNA gene amplicon sequencing and microarray-based approach to reveal the stratification of microorganisms related to C, N and S cycles along vertical redox gradients in intertidal wetlands. Alpha-diversity of bacteria and archaea was generally higher at the deep groundwater-sediment interface. Microbial compositions were markedly altered along the sediment profile, and these shifts were largely due to changes in nutrient availability and redox potential. Furthermore, functional genes exhibited redox partitioning between interfaces and transition layer, with abundant genes involved in C decomposition, methanogenesis, heterotrophic denitrification, sulfite reduction and sulfide oxidation existed in the middle anoxic zone. The influence of tidal dynamics on sediment function was highly associated with redox state, sediment texture, and substrates availability, leading to distinct distribution pattern of metabolic coupling of microbes involved in energy flux and elemental cycling in intertidal wetlands. These results indicate that tidal cycles are critical in determining microbial community and functional structure, and they provide new insights into sediment microbe-mediated biogeochemical cycling in intertidal habitats.

Distinct patterns of distribution, community assembly and cross-domain co-occurrence of planktonic archaea in four major estuaries of China

BACKGROUND

Archaea are key mediators of estuarine biogeochemical cycles, but comprehensive studies comparing archaeal communities among multiple estuaries with unified experimental protocols during the same sampling periods are scarce. Here, we investigated the distribution, community assembly, and cross-domain microbial co-occurrence of archaea in surface waters across four major estuaries (Yellow River, Yangtze River, Qiantang River, and Pearl River) of China cross climatic zones (~ 1,800 km) during the winter and summer cruises.

RESULTS

The relative abundance of archaea in the prokaryotic community and archaeal community composition varied with estuaries, seasons, and stations (reflecting local environmental changes such as salinity). Archaeal communities in four estuaries were overall predominated by ammonia-oxidizing archaea (AOA) (aka. Marine Group (MG) I; primarily Nitrosopumilus), while the genus Poseidonia of Poseidoniales (aka. MGII) was occasionally predominant in Pearl River estuary. The cross-estuary dispersal of archaea was largely limited and the assembly mechanism of archaea varied with estuaries in the winter cruise, while selection governed archaeal assembly in all estuaries in the summer cruise. Although the majority of archaea taxa in microbial networks were peripherals and/or connectors, extensive and distinct cross-domain associations of archaea with bacteria were found across the estuaries, with AOA as the most crucial archaeal group. Furthermore, the expanded associations of MGII taxa with heterotrophic bacteria were observed, speculatively indicating the endogenous demand for co-processing high amount and diversity of organic matters in the estuarine ecosystem highly impacted by terrestrial/anthropogenic input, which is worthy of further study.

CONCLUSIONS

Our results highlight the lack of common patterns in the dynamics of estuarine archaeal communities along the geographic gradient, expanding the understanding of roles of archaea in microbial networks of this highly dynamic ecosystem.

Chemodiversity of Dissolved Organic Matter Is Governed by Microbial Biogeography in Inland Waters

Dissolved organic matter (DOM) is crucial for the carbon biogeochemical cycle and has a close link with microbiome in aquatic ecosystems; however, the causal relationship between DOM and microbial diversity in inland waters is not very clear so far. Therefore, a national survey of China's inland waters was conducted, and the DOM chemical composition and microbial community composition were determined by Fourier transform ion cyclotron resonance mass spectrometry and high-throughput sequencing to clarify the abovementioned question. Here, we found that DOM chemodiversity was governed by microbial community assembly in inland waters, not vice versa. Under the control of microbial biogeography, DOM chemodiversity showed a clear geographical distribution difference. Water DOM chemodiversity was mainly constrained by bacterial and archaeal community composition, whereas sediment DOM chemodiversity was mainly controlled by eukaryotic and fungal community composition. In addition, the sediment DOM chemical composition was also affected by the interaction of different microbial groups between waters and sediments. The study is the first to clarify the causal relationship and proposes a microbial regulatory mechanism on the geographical distribution pattern of DOM chemodiversity, thus further deepening the understanding of the DOM biogeochemical cycle.

Biogeographic Patterns and Community Assembly Processes of Bacterioplankton and Potential Pathogens in Subtropical Estuaries in China

Microbial communities in coastal waters are diverse and dynamic and play important roles in ecosystem functions and services. Despite the ecological impact of bacterioplankton or pathogens, little is known about whether bacterioplankton and pathogen communities exhibit similar patterns. Here, using 16S RNA gene amplicon sequencing, the geographic patterns and assembly processes of bacterioplankton and pathogen communities in 30 subtropical estuaries were studied. Results showed that the estuarine bacterioplankton communities mainly consisted of Proteobacteria (49.06%), Actinobacteria (17.62%), and Bacteroidetes (16.33%), among which 31 pathogen genera (186 amplicon sequence variants [ASVs]) were identified. Under the influence of salinity, bacterioplankton and pathogens showed similar biogeographic patterns. Redundancy and correlation analyses indicated that the bacterioplankton communities were strongly correlated with estuarine environmental factors, but potential pathogens were less influenced. Co-occurrence network analysis revealed a close relationship between bacterioplankton and potential pathogens, with two pathogens identified as connectors (i.e., ASV340 [Clostridium perfringens] and ASV1624 [Brevundimonas diminuta]), implying potential impacts of pathogens on structure, function, and stability of estuarine bacterioplankton communities. Null-model analysis revealed that deterministic processes (heterogeneous selection) dominated bacterioplankton community assembly, while stochastic processes (undominated effect) shaped the potential pathogen community. Our findings illustrate the biogeographic patterns and community assembly mechanisms of bacterioplankton and pathogens in estuaries, which should provide guidance and a reference for the control of potential pathogenic bacteria. IMPORTANCE Bacterioplankton play an important role in estuarine ecosystem functions and services; however, potentially pathogenic bacteria may exhibit infectivity and pose a serious threat to environmental and human health. In this study, geographic patterns and assembly processes of bacterioplankton communities in 30 subtropical estuaries were explored, and potential pathogenic bacteria in the estuaries were detected and profiled. Our results demonstrate here that bacterioplankton and pathogens show similar biogeographic patterns under the influence of salinity. Interestingly, heterogeneous selection dominated bacterioplankton assembly, while stochasticity dominated pathogen assembly. This study provides important information for future risk assessment of potential pathogenic bacteria as well as management in estuarine ecosystems.

River damming enhances ecological functional stability of planktonic microorganisms

Planktonic microorganisms play an important role in maintaining the ecological functions in aquatic ecosystems, but how their structure and function interrelate and respond to environmental changes is still not very clear. Damming interrupts the river continuum and alters river nutrient biogeochemical cycling and biological succession. Considering that river damming decreases the irregular hydrological fluctuation, we hypothesized that it can enhance the ecological functional stability (EFS) of planktonic microorganisms. Therefore, the community composition of planktonic bacteria and archaea, functional genes related to carbon, nitrogen, sulfur, and phosphorus cycling, and relevant environmental factors of four cascade reservoirs in the Pearl River, Southern China, were investigated to understand the impact of damming on microbial community structure and function and verify the above hypothesis. Here, the ratio of function to taxa (F:T) based on Euclidean distance matrix analysis was first proposed to characterize the microbial EFS; the smaller the ratio, the more stable the ecological functions. The results showed that the reservoirs created by river damming had seasonal thermal and chemical stratifications with an increasing hydraulic retention time, which significantly changed the microbial structure and function. The river microbial F:T was significantly higher than that of the reservoirs, indicating that river damming enhances the EFS of the planktonic microorganisms. Structural equation modeling demonstrated that water temperature was an important factor influencing the relationship between the microbial structure and function and thus affected their EFS. In addition, reservoir hydraulic load was found a main factor regulating the seasonal difference in microbial EFS among the reservoirs. This study will help to deepen the understanding of the relationship between microbial structure and function and provide a theoretical basis of assessing the ecological function change after the construction of river damming.

Archaeal contribution to carbon-functional composition and abundance in China's coastal wetlands: Not to be underestimated

Microbial diversity, together with carbon function, plays a key role in driving the wetland carbon cycle; however, the composition, driving factors of carbon-functional genes and the relationship with microbial community have not been well characterized in coastal wetlands. To understand these concerns, microbes, carbon-functional genes, and related environmental factors were investigated in twenty wetlands along China's coast. The results indicate that carbon-functional gene composition is dominated by archaeal rather than bacterial community and that Nanoarchaeaeota is the dominant archaeal phylum associated with carbon cycling in anoxic sediments. Compared with microbes, carbon-functional composition was more stable because they showed the highest Shannon diversity and archaeal functional redundancy. Deterministic processes dominated microbial community, and stochastic processes were more important for carbon-functional genes. Labile Fe governed archaeal and carbon-functional composition by coupling with nitrogen and carbon biogeochemical cycles, while bacterial community was affected by NH4-N and SOC/SON. This study highlights the predominant contributions of archaea to carbon-functional genes and to the stability of carbon-functional composition, thus providing new insights into the microbial dominance of the carbon cycle and the evaluation of carbon function in coastal wetlands.

Spatiotemporal dynamics, community assembly and functional potential of sedimentary archaea in reservoirs: coaction of stochasticity and nutrient load

Archaea participate in biogeochemical cycles in aquatic ecosystems, and deciphering their community dynamics and assembly mechanisms is key to understanding their ecological functions. Here, sediments from 12 selected reservoirs from the Wujiang and Pearl River basins in southwest China were investigated using 16S rRNA Illumina sequencing and quantitative PCR for archaeal abundance and richness in all seasons. Generally, archaeal abundance and α-diversity were significantly correlated with temperature; however, β-diversity analysis showed that community structures varied greatly among locations rather than seasons, indicating a distance-decay pattern with geographical variation. The null model revealed the major contribution of stochasticity to archaeal community assembly, which was further confirmed by the neutral community model that could explain 71.7% and 90.2% of the variance in archaeal assembly in the Wujiang and Pearl River basins, respectively. Moreover, sediment total nitrogen and organic carbon levels were significantly correlated with archaeal abundance and α-diversity. Interestingly, these nutrient levels were positively and negatively correlated, respectively, with the abundance of methanogenic and ammonia-oxidized archaea: the dominant sedimentary archaea in these reservoirs. Taken together, this work systematically characterized archaeal community profiles in reservoir sediments and demonstrated the combined action of stochastic processes and nutrient load in shaping archaeal communities in reservoir ecosystems.

Co-Occurrence Relationship and Stochastic Processes Affect Sedimentary Archaeal and Bacterial Community Assembly in Estuarine-Coastal Margins

Sedimentary microorganisms play crucial roles in maintaining the functional stability of aquatic ecosystems. However, their taxonomic composition and assembly processes are not well known in estuarine−coastal margins because of their complex environment. We investigated microbial communities, co-occurrence relationships, and underlying mechanisms in 33 surface sediment samples collected in the Jiulong River Estuary and the Taiwan Strait to reveal their composition dynamics. The abundance, diversity, and composition of microorganisms demonstrated obvious spatial variables. Methanobacterium and Methanosarcina, as well as Candidatus_Nitrosopumilus and Nitrososphaeraceae were the main methanogenic and ammonia-oxidizing archaea, with an average abundance of more than 5.91% and 4.27%, respectively. Along with a salinity gradient increase, the relative abundance of methanogenic archaea (from 42.9% to 16.6%) contrasted with the trend of ammonia-oxidizing archaea (from 6.04% to 18.7%). The number of methanogenic archaea gradually decreased with increasing geographic distance (p < 0.05), whereas ammonia-oxidizing archaea showed no significant change (p > 0.05). In co-occurrence patterns, closer inter-taxa connections were observed among archaea−archaea and bacteria−bacteria than in archaea−bacteria, which indicated that coexistence within the same kingdom was greater than interaction between different kingdoms in shaping the community structure along the salinity gradient. Furthermore, null model analyses of the microbial community showed that undominated was the most prominent process, explaining over 44.9% of community variation, followed by heterogeneous selection and dispersal limitation, which contributed to 27.7% and 16.3%, respectively. We demonstrated that stochasticity, rather than determinism, regulates community assembly. These results further highlight that intra-kingdom co-occurrence and stochastic processes shape the structure and assembly of microbial communities in estuarine−coastal margins.