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.