1. Introduction
Sediments, serving as sinks or sources for nutrient cycling (Jozsa et al., 2014), are one of the most diverse microbial habitats in aquatic ecosystems (Lozupone and Knight, 2007). Microorganisms attached to the sediments are critical drivers of biogeochemical processes and play a significant role in food webs and the functioning of aquatic ecosystems (Battin et al., 2009; Handley et al., 2013; Nealson, 1997). Meanwhile, sediment microorganisms are sensitive indicators of environmental change in aquatic ecosystems (Liu et al., 2018; Mason et al., 2014). Sediment microbial biodiversity has been shown to be closely correlated with surrounding heterogeneous landscapes, water quality, land uses, and geomorphology (Hu et al., 2014; Ibekwe et al., 2016; Zhang et al., 2021b). Therefore, deciphering the fundamental mechanisms for maintaining and generating sediment microbial biodiversity is critical for predicting the relationships between microbial community function and environmental processes in changing aquatic ecosystems.
In natural ecosystems, microbial communities are often comprised of relatively few abundant taxa co-existing with a large number of rare taxa, the latter often known as the “rare biosphere” (Jia et al., 2018; Pedrós-Alió, 2012). Previous studies have increasingly emphasized the ecological importance of the rare biosphere in community functioning and stability (Jousset et al., 2017; Lynch and Neufeld, 2015). For example, rare taxa can serve as “seed bank” for maintaining microbial diversity (Galand et al., 2009; Shade et al., 2014), and perform a disproportionate amount of work, as compared to their abundance, in regulating ecosystem functioning (Pester et al., 2010). It has previously been observed that abundant and rare taxa have different ecological responses to environmental changes and often show different distribution patterns and functional traits (Jiao and Lu, 2020; Liu et al., 2015; Wan et al., 2021a; Wan et al., 2021b; Wan et al., 2021c; Xue et al., 2018). For instance, recent evidence suggests that in Tibetan Plateau wetland soils, abundant bacteria are primarily influenced by dispersal limitation, while rare bacteria are mainly governed by environmental filtering (Wan et al., 2021a).
It is now well established from a variety of studies, that the biogeographic patterns of abundant and rare microbial taxa are mainly shaped by deterministic and stochastic processes (Ji et al., 2020; Jiao and Lu, 2020; Mo et al., 2018; Wan et al., 2021a; Xue et al., 2018). Traditionally, deterministic processes refer to nonrandom and niche-based mechanisms, including environmental filtering and various biotic interactions (e.g., competition, predation, and mutualism) (Fargione et al., 2003; Stegen et al., 2015). In contrast, stochastic processes emphasize that community structures are independent of species traits and are instead shaped by processes of birth, death, colonization, extinction, and speciation (Volkov et al., 2003; Zhou and Ning, 2017). Data from several studies suggest that rare taxa are shaped to a far greater degree by environmental filtering than abundant taxa in ocean surface waters (Wu et al., 2017) and in agricultural soils (Jiao and Lu, 2020). However, contrasting results were found in a subtropical reservoir (Xue et al., 2018) and Tibetan Plateau grassland soils (Ji et al., 2020), where communities of rare taxa were driven by stochastic processes more than abundant communities. These results indicate that community assembly of the abundant and rare bacteria may vary with ecosystem and organism types. To date, very little is currently known about the relative impacts of deterministic and stochastic processes on microbial communities in plateau river sediments and the underlying factors.
Environmental filtering is an important determinant in shaping distribution patterns of abundant and rare taxa in aquatic ecosystems (Liu et al., 2019; Liu et al., 2015; Xue et al., 2018). The concept of environmental filtering proposes that changes in species abundances and diversity patterns along environmental gradients, such as sediment pH, temperature, and nitrogen compounds concentration, are based on their traits and adaptations to the prevailing environmental conditions (Wang et al., 2020b; Xiong et al., 2012; Zhang et al., 2021b). It has been reported that abundant taxa exhibit stronger environmental adaptation compared to rare taxa (Jiao and Lu, 2020; Wan et al., 2021a). To be specific, abundant taxa exhibited broader environmental thresholds and stronger phylogenetic signals for ecological preferences across environmental gradients than rare taxa. These studies provided new insights into considering species niche breadth and phylogenetic patterns of microbial response traits for studying the biogeography of abundant and rare taxa and their responses to environmental change. Apart from environmental filtering, biotic interactions are important as a part of deterministic processes in governing distribution patterns and community assemblies of abundant and rare taxa in aquatic ecosystems (Xue et al., 2018; Zhang et al., 2020; Zhou et al., 2020). Analysis of potential interactions between microbial taxa in complex and different microbial communities can help to explore potential functions or environmental niches occupied by microbes (Deng et al., 2012; Hu et al., 2017; Meyer et al., 2020). Furthermore, topology-based analysis of microbial networks is a powerful method for studying the characteristics of co-occurrence patterns at various taxonomic levels and identification of keystone species that play irreplaceable roles in maintaining the stability and function of the microbial community (Ma et al., 2016; Sun et al., 2021).
As the “Water Tower of Asia”, the Tibetan Plateau feeds many large rivers in Asia and benefits billions of people in the surrounding regions (Immerzeel et al., 2010). Among those rivers originating from the Tibetan Plateau, th­e Yarlung Tsangpo River is the longest plateau river in China. The Yarlung Tsangpo plays an important role in the regional water supply and its annual runoff on the plateau is estimated to be 1.65× 1011 m3 (Liu, 1999). The water resources in this river are vital for sustaining the health of regional socioeconomic developments and ecosystem functioning and peoples’ lives on the Tibetan Plateau. Over the past few decades, the Yarlung Tsangpo River has been experiencing dramatic land surface environment changes under the impact of climate change (e.g., glacier retreat and permafrost degradation) and intensified anthropogenic disturbances (e.g., land use change, wastewater discharge and river damming) (Cui et al., 2006; Wang et al., 2020b; Yao et al., 2010). These changes directly impact the water quality and microbial biodiversity of this river, and finally affect its ecosystem functions and reduce ecosystem services. A few studies have been conducted to elucidate the influences of river damming (Wang et al., 2017; Wang et al., 2020b; Wang et al., 2021) or antibiotic resistance genes (Liu et al., 2021) on the diversity, composition, and function of bacterial communities in the Yarlung Tsangpo River. However, the mechanisms for generating and maintaining microbial diversity remain unclear, particularly those of the abundant and rare taxa in the sediments of the Yarlung Tsangpo River.
To address this gap, we used Illumina sequencing of the V4-V5 region of the 16S rRNA gene to investigate the geographic patterns and underlying mechanisms of abundant and rare bacteria in Yarlung Tsangpo River sediments. The main objectives of this study were to i) evaluate environmental adaptations of abundant and rare bacteria; ii) determine the effects of physicochemical factors and surrounding land use types on the geographic patterns of abundant and rare bacterial taxa; and iii) identify the controlling mechanisms and key environmental variables that influence the geographic patterns of abundant and rare bacterial taxa in sediments of the Yarlung Tsangpo River. Given that the narrow niches and low growth rate of rare taxa (Jousset et al., 2017), we hypothesized that rare bacterial taxa would exhibit weaker environmental adaptation compared with abundant taxa. We also hypothesized that the assembly processes underlying abundant and rare taxa were influenced by different environmental variables.