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

Abstract

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.

Spatial patterns in host-associated and free-living bacterial communities across six temperate estuaries

“…For sediment communities, significant associations between community similarity and environmental variables were only documented at larger spatial scales, indicating that these communities may be less strongly influenced by dispersal than environmental filtering across larger spatial scales. Here, salinity was most frequently associated with sediment microbial community diversity and composition, consistent with findings from other systems (Webster et al 2015 , Vekeman et al 2016 , Huang et al 2019 , Yue et al 2022 ). The most abundant ASVs belonging to taxa within the Proteobacteria ( Methyloceanibacter and Woeseia ) and Actinobacteria (Propionibacteriaceae and Actinomarinales) were significantly correlated with salinity and are abundant in estuarine sediments, likely carrying out diverse ecological functions including denitrification, sulfur oxidation, and aerobic ammonium oxidation (Vekeman et al 2016 , Mußmann et al 2017 , Rios-Del Toro et al 2018 , Zhang et al 2020 ).…”

“…Previous findings also indicate, however, that there is a large amount of unexplained variation in these communities, consistent with findings here. These studies suggest that this is a result of either unmeasured environmental variability or stochastic processes such as ecological drift or random speciation and extinction (Martiny et al 2011 , Xiong et al 2014 , Yue et al 2022 , Zhang et al 2022 ).…”

Salinity causes differences in stratigraphic methane sources and sinks

“…One possible reason is that while methanogenesis is inhibited by SO 4 2− reduction at higher SO 4 2− concentrations, this effect is attenuated by high levels of organic matter [ 72 ]. In addition, the concentration of the electron acceptors NO 3 − and SO 4 2− increased with increasing salinity, promoting AOM [ 73 ], thus resulting in a 687.34% higher total methane oxidation rate and 146.31% lower total methane emission in the coastal strata as compared with the terrestrial strata ( Fig. 1 a,c).…”

Differences in Juniperus przewalskii Rhizosphere Microbiomes across Age Classes: Community Diversity and Assembly

“…The primary network nodes belonged to Proteobacteria, Actinobacteria, Acidobacteria, Ascomycota, and Basidiomycota ( Figure 3 a,b), further suggesting that Proteobacteria, Actinobacteria, and Acidobacteria were the most abundant bacterial phyla, and Ascomycota and Basidiomycota were the most abundant fungal phyla. These dominant phyla taxa play vital roles in maintaining the structure and function of soil ecosystems [ 17 , 18 ].…”

“…In soil ecosystems, microbial species coexist in complex arrays through positive (e.g., symbiosis) and negative (e.g., competition) associations [ 17 , 18 ], which can regulate the microbial community structure and thus adjust the functions it provides to the ecosystem [ 19 , 20 ]. Co-occurrence networks are increasingly used to infer linkages among microbial species in many different environments, including the human gut [ 21 ], oceans [ 22 ], and soils [ 23 , 24 , 25 , 26 ].…”