Spatial and temporal changes in microbial diversity of the Marmara Sea sediments

Influences of the Integrated Rice-Crayfish Farming System with Different Stocking Densities on the Paddy Soil Microbiomes

Integrated rice-fish farming has emerged as a novel agricultural production pattern to address global food security challenges. Aiming to determine the optimal, scientifically sound, and sustainable stocking density of red claw crayfish (Cherax quadricarinatus) in an integrated rice-crayfish farming system, we employed Illumina high-throughput 16S rRNA gene sequencing to evaluate the impact of different stocking densities of red claw crayfish on the composition, diversity, function, and co-occurrence network patterns of soil bacterial communities. The high stocking density of red claw crayfish reduced the diversity and evenness of the soil bacterial community during the mid-culture stage. Proteobacteria, Actinobacteria, and Chloroflexi emerged as the most prevalent phyla throughout the experimental period. Low stocking densities initially boosted the relative abundance of Actinobacteria in the paddy soil, while high densities did so during the middle and final stages. There were 90 distinct functional groups identified across all the paddy soil samples, with chemoheterotrophy and aerobic chemoheterotrophy being the most abundant. Low stocking densities initially favored these functional groups, whereas high densities enhanced their relative abundances in the later stages of cultivation. Medium stocking density of red claw crayfish led to a more complex bacterial community during the mid- and final culture stages. The experimental period showed significant correlations with soil bacterial communities, with total nitrogen (TN) and total phosphorus (TP) concentrations emerging as primary factors contributing to the alterations in soil bacterial communities. In summary, our findings demonstrated that integrated rice-crayfish farming significantly impacted the soil microbiomes and environmental factors at varying stocking densities. Our study contributed to theoretical insights into the profound impact of integrated rice-crayfish farming with various stocking densities on bacterial communities in paddy soils.

Impact of mixing on water quality in the Bosphorus - Implications on sustainable management of wastewater marine discharges

The study established the water quality modelling of the Bosphorus system, based on hydrodynamic data as well as the results of the water quality survey carried out in the last five years. The model revealed significant decrease in the magnitude of pollutant loads in the upper layer at the exit into The Marmara Sea providing numerical proof that no pollutant transport would take place from sewage discharges to the upper layer. A similar modelling approach was implemented at the Bosphorus/Marmara interface, a significant hotspot as it included two major deep marine outfalls. The results asserted that the entire sewage flow would enter the lower flow in The Bosphorus through the interface without an appreciable mixing with the upper flow. This way, the study provided a significant scientific support for the sustainable management of marine discharges in this area, since they have no physical interference with The Marmara Sea.

Effects of Bellamya purificata Cultivation at Different Stocking Densities on the Dynamics and Assembly of Bacterial Communities in Sediment

To optimize the integrated multi-trophic aquaculture (IMTA) model, improve the efficiency of resource utilization, and reduce environmental pollution, Bellamya purificata, as a potential bioremediation species, was studied to investigate the effect of B. purificata culture on the dynamics and assembly of bacterial communities in sediment. Four experimental groups were established at four different densities: 0, 234.38, 468.75, and 937.5 g/m² (represented as CON, LD, MD, and HD, respectively). Each group was with three replicates. The 16S ribosomal RNA (rRNA) high-throughput sequencing was used to evaluate the composition, function, and assembly of bacterial communities in sediment. B. purificata cultivation significantly altered the composition and function of the bacterial communities in sediment; at high stocking density, it significantly decreased anaerobic and increased aerobic organic matter decomposition, whereas at low stocking density, it decreased the number of bacteria involved in sulfate reduction and inhibited the denitrification process. B. purificata decreased direct competition and promoted collaboration or niche sharing in bacterial communities, especially at the high stocking density. Moreover, B. purificata cultivation resulted in greater changes in the environmental factors. Variations in dissolved oxygen, pH, total nitrogen, nitrate, and nitrite levels were closely related to the altered composition and function of the bacterial communities. Stochastic processes dominated the bacterial community assembly in the sediment and B. purificata cultivation had limited impacts on the bacterial community assembly. The study provided a reference for the dynamics and assembly of bacterial communities in sediment with different densities of B. purificata cultivation and we hope that the findings will provide a theoretical reference for the optimization of IMTA and improve management strategies for B. purificata polyculture.

Exploring the impacts of physicochemical characteristics and heavy metals fractions on bacterial communities in four rivers

Heavy metals contamination in sediment poses serious threats to bacterial communities that play critical roles in sediment biogeochemical processes. However, the physicochemical factors and the major heavy metals fractions that affect sediment bacterial communities are still unclear. Here, we performed heatmap and redundancy analyses to examine the effects of physico-chemical characteristics and heavy metals fractions on the sediment bacterial community from rivers in the UK (River Tyne and Ouseburn) and India (River Ganga and Yamuna). The results revealed that physicochemical characteristics and heavy metals fractions altered the diversity, richness, and structures of the bacterial community. Moreover, the fractions of Co, Zn, Pb, Cr, and Cu played significant roles in shaping the bacterial community structure, and physicochemical variables, particularly NH₄⁺-N and NO₂^--N, also influenced the bacterial diversity and structure. Firmicutes showed strong associations with both physicochemical factors and heavy metals fractions. Chloroflexi and Actinobacteriota can be used as biomarkers for Zn contamination. Overall, our study identified the significance of sediment chemical characteristics and heavy metals fractions in determining the bacterial community structure as well as bioremediation and environmental management of metals contaminated sites.

Pollutant dynamics between The Black Sea and The Marmara Sea: Basis for wastewater management strategy

The study evaluated pollutant dynamics between The Black Sea and The Marmara Sea using data collected during a marine survey of the region around The Bosphorus strait, in the last five years. A hydraulic model was utilized to define two-layered water exchange in The Bosphorus. Analysis of pollutant exchange indicated The Black Sea as major polluter for the marine environment in The Marmara Sea. Four wastewater outfalls are located along The Bosphorus; Mass balances between the two ends of The Bosphorus indicated losses of 44 t/d total N and 138 t/d COD in the lower layer before reaching The Black Sea. This was explained with a simultaneous nitrification-denitrification process sustained in the low oxygen or anoxic zones around the outfalls, implying that a sustainable wastewater strategy should preclude additional treatment for The Bosphorus discharges, since they do not have an appreciable impact on the water quality of the lower flow.

Effects of high-concentration influent suspended solids on aerobic granulation in pilot-scale sequencing batch reactors treating real domestic wastewater

The aim of this study was to investigate the effect of high-influent-concentration suspended solids (SS) on the cultivation, structure and long-term stability of aerobic granular sludge (AGS). Cultivation and long-term stability of AGS were monitored in two pilot-scale sequencing batch reactors fed with raw (R1) and settled (R2) domestic wastewater, representing high and medium SS content, respectively. The real domestic wastewater had high chemical oxygen demand (COD) content (1100 ± 270 mg COD L^-1). Aerobic granular sludge was cultivated in 44 days (R1) and 25 days (R2) under the conditions of high settling velocity (18 m h^-1) and high organic loading rate (OLR) (2.1-2.4 kg COD m³ day). The AGS in both reactors had similar structural properties during long-term operation and remained structurally and functionally stable during the last five months of operation. Comparative evaluation of the results indicated that the high influent SS content of the real domestic wastewater had a positive influence on maintaining significantly lower SVI₃₀ and relatively lower effluent SS concentration. Moreover, a higher influent SS content resulted in smaller mature granules during the stable period. Microbial community analyses helped to understand the aerobic granular sludge structure and showed that the sludge retention time and OLR affected the granular sludge population. The high influent SS increased biomass detachment from the granular sludge surface and caused wash-out of some bacteria colonizing the exterior of the granular sludge.

Anaerobic sulfamethoxazole degradation is driven by homoacetogenesis coupled with hydrogenotrophic methanogenesis

In this study, microbial community dynamics were assessed in two lab-scale anaerobic sequencing batch reactors (ASBRs). One of the reactors was fed by synthetic pharmaceutical industry wastewater with sulfamethoxazole (SMX) as the test reactor and the other without sulfamethoxazole as the control reactor. DNA based DGGE results indicated that Clostiridum sp. became dominant in the SMX reactor while the inoculum was dominated with Firmicutes (61%) and Methanomicrobiales (28%). However their abundances in active community decreased through the last phase. Also the abundance of hydrogenotrophs was high in each phase, while acetoclastic methanogens disappeared in the last phase. Q-PCR analysis revealed that there is a significant reduction in the bacterial community approximately 84%, while methanogens increased to 97% through the operation. Additionally an increase in the expression level of bacterial and methanogenic 16S rRNA (60% and 20%, respectively) was detected. Significant correlation between microbial community and the reactor operation data was found. The study demonstrated that the microbial community maintains the system stability under high antibiotic concentration and long-term operation by homoacetogenesis coupled with hydrogenotrophic methanogenesis.

Distribution and diversity of fungi in freshwater sediments on a river catchment scale

Fungal communities perform essential functions in biogeochemical cycles. However, knowledge of fungal community structural changes in river ecosystems is still very limited. In the present study, we combined culture-dependent and culture-independent methods to investigate fungal distribution and diversity in sediment on a regional scale in the Songhua River catchment, located in North-East Asia. A total of 147 samples over the whole river catchment were analyzed. The results showed that compared to the mainstream, the tributaries have a higher fungal community organization and culturable fungal concentration, but possess lower community dynamics as assessed by denaturing gradient gel electrophoresis (DGGE). Furthermore, phylogenetic analysis of DGGE bands showed that Ascomycota and Basidiomycota were the predominant community in the Songhua River catchment. Redundancy analysis revealed that longitude was the primary factor determining the variation of fungal community structure, and fungal biomass was mainly related to the total nutrient content. Our findings provide new insights into the characteristics of fungal community distribution in a temperate zone river at a regional scale, and demonstrate that fungal dispersal is restricted by geographical barriers in a whole river catchment.

Analysis of the bacterial community in the two typical intertidal sediments of Bohai Bay, China by pyrosequencing

For full understanding of the bacterial community in the intertidal zones of Bohai Bay, China, we used pyrosequencing-based approach to analyze the 16S rRNA gene of bacteria in the sediments from the two typically intertidal zones - Qikou (Qi) and Gaoshaling (Ga). Results showed that, at a 0.03 distance, the sequences from the Qi sediment were assigned to 3252 operational taxonomic units (OTUs) which belong to 34 phyla, 69 classes and 119 genera, while the 3740 OTUs from the Ga sediment were affiliated with 33 phyla, 66 classes and 146 genera. Comparing the bacterial communities inhabiting in the two intertidal sediments, we observed significant difference in the dominant composition and distribution at phylum, class and genus levels. Canonical correspondence analysis (CCA) showed that the median grain size and DO were the most important factors regulating the bacterial abundance and diversity, while the other environmental factors have effects with different degree.

Effects of prokaryotic diversity changes on hydrocarbon degradation rates and metal partitioning during bioremediation of contaminated anoxic marine sediments

We investigated changes of prokaryotic diversity during bioremediation experiments carried out on anoxic marine sediments characterized by high hydrocarbon and metal content. Microcosms containing contaminated sediments were amended with lactose and acetate and incubated in anaerobic conditions up to 60 d at 20 or 35 °C. Microcosms displaying higher degradation efficiency of hydrocarbons were characterized by the dominance of Alphaproteobacteria and Methanosarcinales and the lack of gene sequences belonging to known hydrocarbonoclastic bacteria. Multivariate analyses support the hypothesis that Alphaproteobacteria are important for hydrocarbon degradation and highlight a potential synergistic effect of archaea and bacteria in changes of metal partitioning. Overall, these results point out that the identification of changes in the prokaryotic diversity during bioremediation of contaminated marine sediments is not only important for the improvement of bio-treatment performance towards hydrocarbons, but also for a better comprehension of changes occurring in metal partitioning which affect their mobility and toxicity.