Ecological mechanisms of sedimental microbial biodiversity shift and the role of antimicrobial resistance genes in modulating microbial turnover

Interaction patterns and keystone taxa of bacterial and eukaryotic communities during sulfamethoxazole mineralization in lake sediment

Sulfamethoxazole (SMX) is a common antibiotic pollutant in aquatic environments, which is highly persistent under various conditions and significantly contributes to the spread of antibiotic resistance. Biodegradation is the major pathway to eliminate antibiotics in the natural environment. The roles of bacteria and eukaryotes in the biodegradation of antibiotics have received considerable attention; however, their successions and co-occurrence patterns during the biodegradation of antibiotics remain unexplored. In this study, 13C-labled SMX was amended to sediment samples from Zhushan Bay (ZS), West Shore (WS), and Gonghu Bay (GH) in Taihu Lake to explore the interplay of bacterial and eukaryotic communities during a 30-day incubation period. The cumulative SMX mineralization on day 30 ranged from 5.2 % to 19.3 %, which was the highest in WS and the lowest in GH. The bacterial community showed larger within-group interactions than between-group interactions, and the positive interactions decreased during incubation. However, the eukaryotic community displayed larger between-group interactions than within-group interactions, and the positive interactions increased during incubation. The proportion of negative interactions between bacteria and eukaryotes increased during incubation. Fifty genera (including 46 bacterial and 4 eukaryotic genera) were identified as the keystone taxa due to their dominance in the co-occurrence network and tolerance to SMX. The cumulative relative abundance of these keystone taxa significantly increased during incubation and was consistent with the SMX mineralization rate. These taxa closely cooperated and played vital roles in co-occurrence networks and microbial community interactions, signifying their crucial role in SMX mineralization. These findings broadened our understanding of the complex interactions of microorganisms under SMX exposure and their potential functions during SMX mineralization, providing valuable insights for in situ bioremediation.

Microbial phylogenetic divergence between surface-water and sedimentary ecosystems drove the resistome profiles

Antibiotic pollution and the evolution of antibiotic resistance genes (ARGs) are increasingly viewed as major threats to both ecosystem security and human health, and have drawn attention. This study investigated the fate of antibiotics in aqueous and sedimentary substrates and the impact of ecosystem shifts between water and sedimentary phases on resistome profiles. The findings indicated notable variations in the concentration and distribution patterns of antibiotics across various environmental phases. Based on the partition coefficient (Kd), the total antibiotic concentration was significantly greater in the surface water (1405.45 ng/L; 49.5 %) compared to the suspended particulate matter (Kd = 0.64; 892.59 ng/g; 31.4 %) and sediment (Kd = 0.4; 542.64 ng/g; 19.1 %). However, the relative abundance of ARGs in surface water and sediment was disproportionate to the abundance of antibiotics concentration, and sediments were the predominant ARGs reservoirs. Phylogenetic divergence of the microbial communities between the surface water and the sedimentary ecosystems potentially played important roles in driving the ARGs profiles between the two distinctive ecosystems. ARGs of Clinical importance; including blaGES, MCR-7.1, ermB, tet(34), tet36, tetG-01, and sul2 were significantly increased in the surface water, while blaCTX-M-01, blaTEM, blaOXA10-01, blaVIM, tet(W/N/W), tetM02, and ermX were amplified in the sediments. cfxA was an endemic ARG in surface-water ecosystems while the endemic ARGs of the sedimentary ecosystems included aacC4, aadA9-02, blaCTX-M-04, blaIMP-01, blaIMP-02, bla-L1, penA, erm(36), ermC, ermT-01, msrA-01, pikR2, vgb-01, mexA, oprD, ttgB, and aac. These findings offer a valuable information for the identification of ARGs-specific high-risk reservoirs.

Vertical changes in water depth and environmental variables drove the antibiotics and antibiotic resistomes distribution, and microbial food web structures in the estuary and marine ecosystems

The influence of vertical changes in water depth on emerging pollutants distribution and microbial food web remains elusive. We investigated the influence of vertical transition in water depth on the environmental variables, antibiotics and antibiotic resistomes, and microbial community structures in estuary and marine ecosystems (0-50 m). Stepwise multiple linear regression model showed that among investigated environmental variables, change in water salinity was the most influential factor dictating the fluoroquinolone and macrolides concentrations, while dissolved oxygen and turbidity were the key influencers of sulfonamides and beta-lactam concentrations, respectively. Bacterial and eukaryotic diversity and niche breadth significantly increased with the increasing water depth. Ecosystem food web structure at the bottom depths was more stable than at the middle and surface depths. At the surface depth, the top 5 keystone genera were Cryothecomonas, Syndiniales, Achromobacter, Pseudopirsonia, and Karlodinium. Whereas Eugregarinorida, Neptuniibacter, Mychonastes, Novel_Apicomplexa_Class_1, Aplanochytrium and Dietzia, Halodaphnea, Luminiphilus, Aplanochytrium, Maullinia dominated the top 5 genera at the middle and the bottom depth, respectively. Absolute abundance of antibiotic resistance genes (ARGs) was drastically increased at the surface depth compared with the middle and bottom depths. Abundance of the top 10 ARGs and mobile genetic elements (MGEs) detected including tnpA-05, aadA2-03, mexF, aadA1, intI-1(clinic), qacEdelta1-02, aadA-02, qacEdelta1-01, cmlA1-01, and aadA-01 were amplified at the surface depth. This study demonstrated that ARGs abundance was disproportionate to bacterial diversity, and anthropogenic disturbances, confinement, MGEs, and ecosystem stability play primary roles in the fate of ARGs. The findings of this study also implicate that vertical changes in the water depth on environmental conditions can influence antibiotic concentrations and microbial community dramatically.