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Microbial abundance and diversity investigations along rivers: Current knowledge and future directions

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Abstract Microbial abundance and diversity in river ecosystems are being increasingly investigated, yet a synthesized understanding is still lacking. Here, studies of microbial abundance and diversity along global rivers are systematically reviewed based on 814 investigations performed across 8376 sites. We found that riverine microbial investigations are extremely heterogeneous regarding the spatiotemporal distribution of the sampling sites, the environmental media concerned, the microbial groups and indices targeted, the methods used, and the physicochemical properties examined. More than 72.23% of the studies were performed in the last 8 years, with most studies conducted in Europe, China, and the United States, while other regions were poorly investigated. Most studies have examined microbes in water, but very few studies have systematically investigated microbes in water, sediments, and riparian soils. Bacteria are the most studied microbial taxonomic groups; microbes with resistance genes and nitrogen cycling genes are the most studied microbial functional groups. High‐throughput sequencing has greatly expanded our understanding of microbial diversity along rivers. Nevertheless, the ecological implications of microbial diversity are still poorly understood. Regarding physicochemical properties, researchers tend to examine environmental parameters that are critical for shaping microbial communities, such as pH, nitrogen, and phosphorus. Future research should pay more attention to rivers that have not been well studied, especially large rivers. Additionally, microbial studies along rivers should be conducted in a more systematic way, taking the underinvestigated environmental media, microbial groups, microbial indices, and physicochemical properties into consideration. Advanced microbiology techniques, such as multiple omics technologies, should be increasingly applied. This article is categorized under: Water and Life > Conservation, Management, and Awareness Water and Life > Nature of Freshwater Ecosystems
The geographic distribution of riverine microbial study sites. (a) All riverine microbial study sites; (b) riverine microbial study sites before 2005; (c) riverine microbial study sites during 2005–2012; (d) riverine microbial study sites after 2012
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(a) The spatial distribution of the proportions of physicochemical properties determined in microbial studies along rivers. (b) the temporal shifts in the proportions of physicochemical properties determined in microbial studies along rivers. AFDW: ash‐free dry weight; ORP: oxidation–reduction potential; oxygen: dissolved oxygen; sulfur: SO42−; chlorine: Cl; nitrogen: total nitrogen, total dissolved nitrogen, NO3‐N, NH4+‐N, and NO2‐N; phosphorous: total phosphorus, PO33−, soluble reactive phosphorus, and total dissolved phosphorus; carbon: total carbon, dissolved organic carbon, and total organic carbon; and solids: total dissolved solids and suspended solids
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The number of riverine microbial study sites where each technology was used. PCR, polymerase chain reaction; qPCR, quantitative PCR; DGGE, denaturing gradient gel electrophoresis; ARISA, automated ribosomal intergenic spacer analysis; T‐RFLP, terminal restriction fragment length polymorphism; and dd‐PCR, droplet digital PCR
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(a) The spatial distribution of the proportions of microbial indices studied along rivers. (b) the temporal shifts in the proportions of microbial indices studied along rivers. The proportions were calculated based on the number of study sites
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The relationships between the microbial groups and the indices examined in riverine microbial studies. (a) The relationships between microbial taxonomic groups and the indices examined; (b) the relationships between microbial functional groups and the indices examined. VR, virus; PO, protozoa; PE, prokaryotes and eukaryotes; OT, other taxonomic microbes; MC, microbes with carbon cycling genes; MS, microbes with sulfur cycling genes; MI, microbes with iron cycling genes; pα, phylogenetic α diversity; pβ, phylogenetic β diversity; fd, functional diversity; bm, biomass; ca, community assembly; co, co‐occurrence among different microbial taxa; pt, phylogenetic classification; and oi, other indices. The numbers on the axes show the number of study sites
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The relative research efforts dedicated to different microbial taxonomic groups (a) and functional groups (b) along the top 35 rivers. The pie charts on the map show the proportions of different microbial groups studied along each river. The size of the pies is proportional to the number of study sites
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The environmental media included in riverine microbial studies. (a) The number of sites where each riverine environmental medium was examined. (b) The number of sites where water, sediments, and soils were examined individually and in combination. (c) The number of papers examining each riverine environmental medium. (d) The number of papers examining water, sediments, and soils individually and in combination. (e) The spatial distribution of the proportions of environmental media in which microbes were examined. (f) The temporal shifts in the percentages of environmental media in which microbes were examined. The proportions in (e) and (f) were calculated based on the study sites. Biofilm, leaves, fine benthic organic matter (FBOM), and coarse benthic organic matter (CBOM) were summarized as others
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