Anthropogenic effects on bacterial diversity and function along a river‐to‐estuary gradient in Northwest Greece revealed by metagenomics

Abstract

Studies assessing the effects of anthropogenic inputs on the taxonomic and functional diversity of bacterioplankton communities in lotic ecosystems are limited. Here, we applied 16S rRNA gene amplicon and whole-genome shotgun sequencing to examine the microbial diversity in samples from the Kalamas River (Northwest Greece), a mid-size river that runs through agricultural and NATURA-protected areas, but also receives urban sewage from a large city through a manmade ditch. Samples from three different locations between the exit of the ditch and the estuary, during three different months showed that temporal differences of taxonomic and functional diversity were more pronounced than spatial ones, and <1% of total taxa were shared among all samples, revealing a highly dynamic ecosystem. Comparisons of gene diversity with other aquatic habitats showed that only the high flow winter samples resembled more to freshwater environments while samples during the decreased water flow months were dominated by sewage inputs and soil-related organisms. Notably, microbial human gut signals were detectable over background freshwater and soil/runoff related signals, even at tens of kilometers downstream the city. These findings revealed the significance of allochthonous inputs on the composition and dynamics of river bacterial communities, and highlighted the potential of metagenomics for source tracking purposes.

Exploring the Impacts of Anthropogenic Disturbance on Seawater and Sediment Microbial Communities in Korean Coastal Waters Using Metagenomics Analysis

“…Coastal microbial communities are highly dynamic over space and time in response to environmental heterogeneities such as day length, temperature, water depth, oceanic currents, and inorganic nutrients [13,14]. During the last decade, a number of studies on natural microbial communities in marine environments have been performed using an NGS-based metagenomics approach to explore the diversity, community structure or composition, and its seasonal variation from various oceanic regions worldwide (e.g., [13,23,24,28,37,38]), yet, relatively little attention has been paid to the impacts of anthropogenic disturbances such as “sand mining” activity on the marine ecosystem using genomic DNA analysis from a whole microbial community [9,10,18,19]. A recent study with a metagenomics approach revealed that shifts in microbial composition within Sydney Harbor, Australia, which is one of the most anthropogenically highly impacted urban estuaries, were strongly linked to an enrichment of total microbial metabolic pathways including phosphorus and nitrogen metabolism, sulfate reduction, virulence, and the degradation of hydrocarbons [9].…”

“…Evaluation of the structure and diversity of microorganisms or bacterial communities in coastal ecosystems has recently been suggested to be critical to gauge their environmental status, particularly for those that have been affected by human-driven stressors [9,10]. Microbial organisms can be a reliable indicator for detecting or diagnosing changes in seawater ecosystems because they are known to be sensitive to hydrologic and water quality changes exhibiting a rapid response to those changes (e.g., [11]).…”

“…Furthermore, it has recently been suggested that “marine metagenomics” is a reliable and novel method for assessing and monitoring environmental health status in the marine ecosystem [28]. Nevertheless, relatively few studies have so far been conducted using metagenomic DNA sequencing (e.g., 16S rRNA) to directly assess the impacts of human activities on the structure and biodiversity of microbial communities in the marine ecosystems [9,10,18,19]. …”

Unraveling the environmental and anthropogenic drivers of bacterial community changes in the Estuary of Bilbao and its tributaries

“…The main tributaries were included in the study and several environmental parameters (such as salinity, temperature, dissolved oxygen concentration, turbidity, pH, and chlorophyll concentration) were observed to give further context to the revealed patterns. High rainfall during the winter and spring, a period of low DO concentration with high levels of chlorophyll and temperature in the inner estuary (B30) in summer [13,15,21,25], and the thermal variation happening from winter to summer—all appeared to correlate with fluctuations in the bacterial community. Despite these various microbial compositions, a similar community makeup was found at both the beginning and end of this yearlong study, suggesting an annual cycling of the microbial community.…”

“…The use of amplicon sequencing to depict the makeup of bacterial communities in urban estuaries has been primarily focused on analyzing large estuaries with a well-defined salinity gradient (mixed or partially-mixed) like that of the Mississippi River in the United States [19], Sydney in Australia [20], and Kalama in Greece [21]. Although these estuaries are composed of dissimilar communities, common patterns can be observed throughout that point to salinity and temperature as main variables defining bacterial community changes in these large estuaries.…”