Effect of River Ecological Restoration on Biofilm Microbial Community Composition

Temporal changes in the morphological and microbial diversity of biofilms on the surface of a submerged stone in the Danube River

Epilithic biofilms are ubiquitous in large river environments and are crucial for biogeochemical processes, but their community structures and functions remain poorly understood. In this paper, the seasonal succession in the morphological structure and the taxonomic composition of an epilithic bacterial biofilm community at a polluted site of the Danube River were followed using electron microscopy, high-throughput 16S rRNA gene amplicon sequencing and multiplex/taxon-specific PCRs. The biofilm samples were collected from the same submerged stone and carried out bimonthly in the littoral zone of the Danube River, downstream of a large urban area. Scanning electron microscopy showed that the biofilm was composed of diatoms and a variety of bacteria with different morphologies. Based on amplicon sequencing, the bacterial communities were dominated by the phyla Pseudomonadota and Bacteroidota, while the most abundant archaea belonged to the phyla Nitrososphaerota and Nanoarchaeota. The changing environmental factors had an effect on the composition of the epilithic microbial community. Critical levels of faecal pollution in the water were associated with increased relative abundance of Sphaerotilus, a typical indicator of "sewage fungus", but the composition and diversity of the epilithic biofilms were also influenced by several other environmental factors such as temperature, water discharge and total suspended solids (TSS). The specific PCRs showed opportunistic pathogenic bacteria (e.g. Pseudomonas spp., Legionella spp., P. aeruginosa, L. pneumophila, Stenotrophomonas maltophilia) in some biofilm samples, but extended spectrum β-lactamase (ESBL) genes and macrolide resistance genes could not be detected.

Microbial community structure and diversity attached to the periphyton in different urban aquatic habitats

Periphyton is a complex community composed of diverse prokaryotes and eukaryotes; understanding the characteristics of microbial communities within periphyton becomes crucial for biogeochemical cycles and energy dynamics of aquatic ecosystems. To further elucidate the community characteristics of periphyton across varied aquatic habitats, including unpolluted ecologically restored lakes, aquaculture ponds, and areas adjacent to domestic and industrial wastewater treatment plant outfalls, we explored the composition and diversity of prokaryotic and eukaryotic communities in periphyton by employing Illumina MiSeq sequencing. Our findings indicated that the prokaryotic communities were predominantly composed of Proteobacteria (40.92%), Bacteroidota (21.01%), and Cyanobacteria (10.12%), whereas the eukaryotic communities were primarily characterized by the dominance of Bacillariophyta (24.09%), Chlorophyta (20.83%), and Annelida (15.31%). Notably, Flavobacterium emerged as a widely distributed genus among the prokaryotic community. Unclassified_Tobrilidae exhibited higher abundance in unpolluted ecologically restored lakes. Chaetogaster and Nais were enriched in aquaculture ponds and domestic wastewater treatment plant outfall area, respectively, while Surirella and Gomphonema dominated industrial sewage treatment plant outfall area. The alpha diversity of eukaryotes was higher in unpolluted ecologically restored lakes. pH and nitrogen content (NO 2 - - N ,NO 3 - - N , and TN) significantly explained the variations for prokaryotic and eukaryotic community structures, respectively. Eukaryotic communities exhibited a more pronounced response to habitat variations compared to prokaryotic communities. Moreover, the association networks revealed an intensive positive correlation between dominant Bacillariophyta and Bacteroidota. This study provided useful data for identifying keystone species and understanding their ecological functions.

Do Microorganisms in Bathing Water in Guadeloupe (French West Indies) Have Resistance Genes?

Waterborne faecal contamination is a major public health concern. The main objectives of this study were to investigate faecal contamination and Escherichia coli (E. coli) antibiotic resistance in recreational fresh water from Guadeloupe and to characterise the microbiome and resistome composition in biofilms from submerged rocks. Significant faecal contamination was observed at 14 freshwater sites. E. coli predominated (62%), followed by Enterobacter cloacae (11%) and Acinetobacter spp. (11%). Of 152 E. coli isolated, none produced extended-spectrum beta-lactamases (ESBLs), but 7% showed resistance to streptomycin and 4% to tetracycline. Biofilm resistome analysis revealed clinically significant antibiotic-resistance genes (ARGs), including those coding for resistance to sulfonamides (sul1), carbapenems (blaKPC), and third-generation cephalosporins (blaCTX-M). Mobile genetic elements (MGEs) (intI1, intI2, intI3) linked to resistance to aminoglycosides, beta-lactams, tetracycline, as well as heavy metal resistance determinants (copA, cusF, czcA, merA) conferring resistance to copper, silver, cadmium, and mercury were also detected. Diverse bacterial phyla were found in biofilm samples, of which Proteobacteria, Bacteroidetes, Planctonomycetes, and Cyanobacteria were predominant. Despite the frequent presence of E. coli exceeding regulatory standards, the low levels of antibiotic-resistant bacteria in freshwater and of ARGs and MGEs in associated biofilms suggest limited antibiotic resistance in Guadeloupean recreational waters.

Implications of Soil Microbial Community Assembly for Ecosystem Restoration: Patterns, Process, and Potential

While it is now widely accepted that microorganisms provide essential functions in restoration ecology, the nature of relationships between microbial community assembly and ecosystem recovery remains unclear. There has been a longstanding challenge to decipher whether microorganisms facilitate or simply follow ecosystem recovery, and evidence for each is mixed at best. We propose that understanding microbial community assembly processes is critical to understanding the role of microorganisms during ecosystem restoration and thus optimizing management strategies. We examine how the connection between environment, community structure, and function is fundamentally underpinned by the processes governing community assembly of these microbial communities. We review important factors to consider in evaluating microbial community structure in the context of ecosystem recovery as revealed in studies of microbial succession: (1) variation in community assembly processes, (2) linkages to ecosystem function, and (3) measurable microbial community attributes. We seek to empower restoration ecology with microbial assembly and successional understandings that can generate actionable insights and vital contexts for ecosystem restoration efforts.

Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater

Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full‐length 16S ribosomal RNA gene Nanopore sequencing and strain‐resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray–Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain‐resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG‐encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.

Water Quality and Microbial Community in the Context of Ecological Restoration: A Case Study of the Yongding River, Beijing, China

Ecological water replenishment via interbasin water diversion projects provides opportunities for ecological river restoration. Untangling water quality changes, microbiota dynamics, and community functions is necessary for sustainable ecological management. Using the Yongding River as a case study, we monitored the water quality and applied genomic sequencing to investigate microbial communities of the river in different stages after ecological water replenishment. Our results showed that river water quality represented by chemical oxygen demand (COD), total nitrogen (TN), and chlorophyll-a (Chl-a) did not change significantly during months after water replenishment. The bacterial community composition varied in different months and river subsections. The Cyanobium_PCC-6307, CL500-29 marine group, and Pseudomonas were dominant in the later stages after water replenishment. Water temperature, pH, and nutrient levels significantly affected the microbial community composition, and ecological restoration may have the potential to influence nitrogen cycling in the river. Our results can provide ecological insights into sustainable water quality maintenance and river management following ecological restoration enabled by ecological water replenishment.

Gradual Enhancement of the Assemblage Stability of the Reed Rhizosphere Microbiome with Recovery Time

Rhizoplane microbes are considered proxies for evaluating the assemblage stability of the rhizosphere in wetland ecosystems due to their roles in plant growth and ecosystem health. However, our knowledge of how microbial assemblage stability is promoted in the reed rhizosphere of wetlands undergoing recovery is limited. We investigated the assemblage stability, diversity, abundance, co-occurrence patterns, and functional characteristics of reed rhizosphere microbes in restored wetlands. The results indicated that assemblage stability significantly increased with recovery time and that the microbial assemblages were capable of resisting seasonal fluctuations after more than 20 years of restoration. The number of bacterial indicators was greater in the restoration groups with longer restoration periods. Most bacterial indicators appeared in the 30-year restoration group. However, the core taxa and keystone species of module 2 exhibited greater abundance within longer recovery periods and were well organized, with rich and diverse functions that enhanced microbial assemblage stability. Our study provides insight into the connection between the rhizosphere microbiome and recovery period and presents a useful theoretical basis for the empirical management of wetland ecosystems.

Response of Coastal Shewanella and Duganella Bacteria to Planktonic and Terrestrial Food Substrates

Global warming scenarios indicate that in subarctic regions, the precipitation will increase in the future. Coastal bacteria will thus receive increasing organic carbon sources from land runoff. How such changes will affect the function and taxonomic composition of coastal bacteria is poorly known. We performed a 10-day experiment with two isolated bacteria: Shewanella baltica from a seaside location and Duganella sp. from a river mouth, and provided them with a plankton and a river extract as food substrate. The bacterial growth and carbon consumption were monitored over the experimental period. Shewanella and Duganella consumed 40% and 30% of the plankton extract, respectively, while the consumption of the river extract was low for both bacteria, ∼1%. Shewanella showed the highest bacterial growth efficiency (BGE) (12%) when grown on plankton extract, while when grown on river extract, the BGE was only 1%. Duganella showed low BGE when grown on plankton extract (< 1%) and slightly higher BGE when grown on river extract (2%). The cell growth yield of Duganella was higher than that of Shewanella when grown on river extract. These results indicate that Duganella is more adapted to terrestrial organic substrates with low nutritional availability, while Shewanella is adapted to eutrophied conditions. The different growth performance of the bacteria could be traced to genomic variations. A closely related genome of Shewanella was shown to harbor genes for the sequestration of autochthonously produced carbon substrates, while Duganella contained genes for the degradation of relatively refractive terrestrial organic matter. The results may reflect the influence of environmental drivers on bacterial community composition in natural aquatic environments. Elevated inflows of terrestrial organic matter to coastal areas in subarctic regions would lead to increased occurrence of bacteria adapted to the degradation of complex terrestrial compounds with a low bioavailability.

Predicting bend-induced heterogeneity in sediment microbial communities by integrating bacteria-based index of biotic integrity and supervised learning algorithms

Prioritizing the relationship between heterogeneity of sediment habitats and river bends is critical when planning and reconstructing urban rivers. However, the exact relationship between ecological heterogeneity and river bends remains ambiguous. Therefore, this research proposed a new approach to quantify and predict bend-induced ecological heterogeneity, incorporating the bacteria-based index of biotic integrity (Ba-IBI), path model, and random forest regression model. The developed Ba-IBI quantified heterogeneity in sediment microbial communities, ranging from low (1.40) to high (3.97). A path model was developed and validated in order to further investigate the relative contributions of environmental factors to the Ba-IBI. The established path model, which was considered acceptable with a CMIN/df = 1.949 < 4, suggested that primary environmental factors affecting the sediment bacterial communities were flow velocity and ammonium concentration in sediment. To further characterize the relationship between environmental factors and the Ba-IBI, a function was constructed using the random forest regression model that predicts the responses of sediment bacterial communities to environmental factors with R² = 0.6126. The proposed approach and prediction tools will provide knowledge to improve natural channel design and post-project evaluations in river restoration projects.

Biofilm Bacterial Dynamics and Changes in Inorganic Nitrogen Density Due to the Presence of Freshwater Pearl Mussels

The freshwater pearl mussel (genus Margaritifera) has shown severe declines, while the mussels play important roles in the translocation of nutrients and materials in river water ecosystems. We hypothesized that the biofilm bacterial composition and nutrient flow may reflect the differences in the existence of mussels. We analyzed water from 14 rivers from in multiple regions of Japan, including eight rivers, where the two species of freshwater pearl mussels (Margaritifera laevis and Margaritifera togakushiensis) are predominantly found, to analyze the microbial and nutritional nature of the biofilm artificially formed in the river. Field-produced biofilms, including the bacterial community structure, were examined, using next-generation sequencing of bacterial 16S rRNA gene amplicons followed by analyzing the genomic DNA extracted from the samples, inorganic nitrogen compounds, and chlorophyll a concentration. Compared to those in the control river without freshwater pearl mussels, biofilms of the existing river contained less inorganic nitrogen (ammonia and nitrate), suggesting the involvement of mussels in regulating the river water nutrient flow. Distinct changes were found in biofilms, depending on mussel existence, particularly in biofilms containing fewer photosynthetic bacterial groups, such as Betaproteobacteria and Cyanobacteria. Conversely, bacteria belonging to Bacteroidales in Bacteroidetes and Clostridiales in Firmicutes were predominantly found in biofilm samples where the mussels existed. Mussels alleviated strict nitrogen limitation in streams and possibly caused a concomitant change in the bacterial communities, where populations of bacterial groups exchanging inorganic nitrogen were low. We demonstrate the profound influence of freshwater mussel species on ecosystem processes and community dynamics across rivers.

IMPORTANCE The abundance of freshwater unioid mussels exhibited more diverse patterns of inorganic nitrogen flow and bacterial communities than the areas without mussels. This study demonstrates the effect of mussels on different freshwater ecosystem processes with variable organismal densities and biogeochemical factors. Freshwater unionid mussels significantly affect the ecosystem and community dynamics by modulating the relationships, altering nutrient availability, and indirectly manipulating the downstream ecological members, eventually expanding their role in the river ecosystems.

The effect of habitat restoration on macroinvertebrate communities in Shaoxi rivers, China

In recent decades, the biodiversity of freshwater environments has decreased sharply due to anthropogenic disturbances that damaged ecosystem structures and functions. Habitat restoration has emerged as an important method to mitigate the degradation of river ecosystems. Although in many cases a post-project monitoring has been promoted to access the restoration progress, it is still unclear how aquatic community changes following river habitat restoration in China. Macroinvertebrate communities intermediately positioned within ecosystem food webs play a key role in ecosystem processes within river ecosystem, driving energy flow and nutrient cycling. Here, benthic macroinvertebrates are used as bio-indicators to assess the ecosystem health of degraded urban rivers, restored urban rivers, and undisturbed rivers. This study aims to determine (i) how habitat restoration influences macroinvertebrates diversity and how this compared to degraded and reference conditions; (ii) how did macroinvertebrate community compositions differ in restored, degraded, and reference sites; and (iii) the environmental factors shaping macroinvertebrate communities. Habitat restoration significantly increased the diversity and richness of macroinvertebrate community and intolerant species and shifted the community composition towards reference status. Habitat characteristics and water chemistry, including substrate diversity, water velocity, and both nutrients (TN) and organic pollutants (TOC), appeared to shape the turnover of these communities. Habitat characteristics contributed to most of the variation of the entire macroinvertebrate community. Our research indicates that habitat restoration is an efficient approach to restore the aquatic community and hence improve river ecosystem health for freshwater conservation and sustainable management in Zhejiang province. This study strengthens our understanding of the changes of macroinvertebrate community after habitat restoration and important controlling variables that attribute to these changes, which provides an important guidance for future freshwater management.

The influence of the environment in the incorporation of copper and cadmium in scraper insects

In regions with intense agricultural activity, increases in heavy metal concentrations in aquatic environments are common. Among the metals associated with agricultural activities, copper (Cu) and cadmium (Cd) have been found to directly affect aquatic trophic structures due to the ease of incorporation by primary producers and consuming organisms. Aquatic insects are predominantly found in streams, and their presence is determined by environmental characteristics and food availability. In this study, we seek to understand how the incorporation of Cu and Cd by scraper insects relates to their environment and food sources. We collected water, sediment, biofilm and scraper insect samples in streams with different intensities of agricultural activities in the drainage areas. The intensity of agricultural activities in the catchment area positively influenced the Cu and Cd concentrations in organisms and other aquatic compartments. The metals were readily incorporated by the biofilms. Although the functional characteristics are important to understand the functioning of ecosystems, in this study, we found that the physiological characteristics can be determinants in the concentrations of metals in aquatic insects.

Evaluating ecosystem functioning following river restoration: the role of hydromorphology, bacteria, and macroinvertebrates

Ecological restoration of freshwater ecosystems is now being implemented to mitigate anthropogenic disruption. Most emphasis is placed on assessing physico-chemical and hydromorphological properties to monitor restoration progress. However, less is known about the structural integrity and ecosystem health of aquatic ecosystems. In particular, little is known about how ecosystem function changes following river habitat restoration, especially in China. Leaf litter decomposition can be used as an indicator of stream ecosystem integrity. Therefore, the leaf breakdown rate was measured to assess the ecosystem function of restored rivers. By comparing leaf breakdown rates in urban rivers undergoing habitat restoration with that in degraded urban rivers and rivers in forested areas (i.e., reference conditions), we aimed to determine: (i) how habitat restoration affected leaf litter decomposition? (ii) the relationship between leaf litter decomposition to both environmental (habitat and physico-chemical variables) and biological factors (benthic communities), and (iii) identify the factors that contribute most to the variance in leaf litter breakdown rates. The results demonstrated a significant increase in leaf breakdown rate (120% in summer and 28% in winter) in the restored rivers compared to the degraded rivers. All environmental and biotic factors evaluated contributed synergistically to the differences in leaf litter decomposition among the three river types. The role of macroinvertebrates, mainly shredders, appeared to be particularly important, contributing 52% (summer) and 33% (winter) to the variance in decomposition, followed by habitat characteristics (e.g. substrate diversity, water velocity; 17% in summer, 29% in winter), physico-chemical variables (e.g. nutrient and organic pollutants; 11% in summer, 1% in winter) and biofilm bacteria (0% in summer, 15% in winter). Habitat restoration positively affected the structure and function of the previously degraded streams. Knowledge on controlling variables and their attribution to changes of ecosystem functioning provides guidance to assist the future planning of ecological restoration strategies.