Sediment Features and Human Activities Structure the Surface Microbial Communities of the Venice Lagoon

Abstract

Sediment microbial communities play essential roles in marine ecosystem functioning. Their study is crucial to understand how environmental conditions affect microbial diversity and biogeochemical cycles. The Venice Lagoon, one of the largest Adriatic transitional systems, is subjected to different natural and anthropogenic stressors. In this study, surface sediments microbial communities were finely characterized using 16S rRNA gene amplicon sequencing and metagenomics. Samples were collected seasonally in 2019 and 2020 at different sites within Lagoon sub-basins. Our results indicated a stable spatial distribution of the sediment microbiome: salinity, grain size, and total organic carbon were found to be important drivers in shaping prokaryotic communities, while temperature had a minor role. We detected high microbial diversity at all stations, mainly due to low abundant taxa: bacteria represented the vast majority of the reads (∼96.1%), with Woeseia the most abundant genus (∼4.4%). The metagenomic analysis highlighted significant differences among sites in terms of biogeochemical processes (e.g., C, N, Fe, and S metabolism), and cell-cell interaction strategies (e.g., mobilome, regulations and cell signaling). Chioggia, a sandy site subjected to marine influence, presented the highest abundance of ammonia-oxidizing archaeon Candidatus Nitrosopumilus, in accordance with the highest amount of ammonia monooxygenase subunit genes. At the same site, sulfate-reducing bacteria (Desulfobacteria and Desulfobacterales) and sulfur-related genes were found in lower abundance. Marghera and Tresse, the most polluted sites, showed higher abundance of sewage-related bacteria and antibiotic and toxic compound resistance genes. Furthermore, these sites showed higher amount of genes related to cell-cell interaction, such as pathogenicity islands, transposable-elements, and biofilm formation. Our findings highlighted that sediment features and human-related activities have profound and long-term impacts on the surface sediment microbial communities of the Venice Lagoon.

Sediment Microbiota as a Proxy of Environmental Health: Discovering Inter- and Intrakingdom Dynamics along the Eastern Mediterranean Continental Shelf

“…The continental shelf of Israel was characterized by several key properties, including particle size distribution, total organic carbon (TOC), water content and carbonate content (150 km north to south) for seafloor depths between 10 m and 100 m, attributing direct correspondence between seafloor depth and the measured parameters ( 28 ). Previous studies of marine and estuarine sedimentary systems show that the properties of sediment are key to determining the composition of microbiota ( 15 , 32 – 35 ). Here, seafloor depth, representing these properties, explained 11% of the variance among samples ( Fig.…”

Microbial Community Diversity of Coral Reef Sediments on Liuqiu Island, Southwestern Taiwan

“…In the sample 201707HFR, the total reads of the putative humanrelated genera accounted for 2.75%, and Desulfococcus was the most abundant genus (2.60%). Desulfococcus is usually found in anaerobic or polluted environments [33,35,122,123]. The unusually abundant putative pathogen and human-related bacteria in samples 201509LC and 201707HFR may imply a sudden outburst of ecological events occurred in 2015 and 2017.…”

Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment

“…In upper oceanic sediments, it has been estimated that microbes represent 5 × 10 28 cells (Flemming and Wuertz 2019 ). Surface sediments are also complex and dynamic habitats, especially in coastal and lagoon environments, where transport, mixing, deposition, and resuspension concur together with other abiotic (e.g., light, organic matter, oxygen) and biotic factors (Zinger et al 2011 ) in shaping microbial assemblages (Banchi et al 2021 ; Quero et al 2017 ). Indeed, the functioning of these ecosystems is highly dependent on microbial communities, which play essential roles in nutrient cycling, organic matter degradation, and benthic food web dynamics (Schallenberg and Kalff 1993 ) and can interact and cope with environmental pressures via fundamental strategies.…”

“…, heavy metals and toxins, accumulated in the sediments after being discharged in the water column) (Depinto et al 2010 ; Solidoro et al 2010 ). Here, in 2019-2020, we conducted a study in which the sediment prokaryotic communities were characterized with DNA metabarcoding and metagenomics (Banchi et al 2021 ). The surface sediment of five sites, distributed in sub-basins of the Lagoon according to the international risk analyses sediment quality guidelines (Apitz et al 2007 ) were investigated: Chioggia, Marghera, Palude della Rosa, Sacca Sessola, and Tresse.…”

“…The surface sediment of five sites, distributed in sub-basins of the Lagoon according to the international risk analyses sediment quality guidelines (Apitz et al 2007 ) were investigated: Chioggia, Marghera, Palude della Rosa, Sacca Sessola, and Tresse. The results highlighted that the microbial communities were significantly influenced by total organic carbon, salinity and grain size, differentiated among sub-basins (mostly due to the rare microbiome), and more stable compared to pelagic communities over time (Banchi et al 2021 ).…”