Effects of the invasive clam Corbicula fluminea (Müller, 1774) on an estuarine microbial community

Intrahabitat Differences in Bacterial Communities Associated with Corbicula fluminea in the Large Shallow Eutrophic Lake Taihu

The Asian clam Corbicula fluminea is a keystone zoobenthos in freshwater ecosystems. However, its associated microbiome is not well understood. We investigated the bacterial communities of this clam and its surrounding environment, including sediment and water simultaneously, in a large lake by means of 16S rRNA gene sequencing. Approximately two-thirds of the bacterial operational taxonomic units (OTUs) associated with clams were observed in the surrounding environment and mostly from particle-associated samples. The associated bacterial communities were site specific and more similar to environmental bacteria from the same site than those at other sites, suggesting a local environmental influence on host bacteria. However, the significant differences in bacterial diversities and compositions between the clam and the environment also indicated strong host selection pressure on bacteria from the surrounding environment. Bacteria affiliated with Firmicutes, Spirochaetes, Tenericutes, Bacteroidetes, Epsilonbacteraeota, Patescibacteria, and Fusobacteria were found to be significantly enriched in the clams in comparison to their local environment. Oligotyping analyses of the core-associated bacterial OTUs also demonstrated that most of the core OTUs had lower relative abundances and occurrence frequencies in environmental samples. The core bacterial OTUs were found to play an important role in maintaining the stability of the bacterial community network. These core bacteria included the two most abundant taxa Romboutsia and Paraclostridium with the potential function of fermenting polysaccharides for assisting host clams in food digestion. Overall, we demonstrate that clam-associated bacteria were spatially dynamic and site specific, which were mainly structured both by local environments and host selection. IMPORTANCE The Asian clam Corbicula fluminea is an important benthic clam in freshwater ecosystems due to its high population densities and high filtering efficiency for particulate organic matter. While the associated microbiota is believed to be vital for host living, our knowledge about the compositions, sources, and potential functions is still lacking. We found that C. fluminea offers a unique ecological niche for specific lake bacteria. We also observed high intrahabitat variation in the associated bacterial communities. Such variations were driven mainly by local environments, followed by host selection pressure. While the local microbes served as a source of the clam-associated bacteria, host selection resulted in enrichments of bacterial taxa with the potential for assisting the host in organic matter digestion. These results significantly advance our current understanding of the origins and ecological roles of the microbiota associated with a keynote clam in freshwater ecosystems.

Microbial community and interspecies interaction during grazing of ark shell bivalve (Scapharca subcrenata) in a full-scale bioremediation system of mariculture effluents

A novel biological approach using ark shell bivalves as potential species for remediation of effluents was studied to determine the microbial community interspecies interaction and nutrient cycling in a restoration system of mariculture effluents. A field study showed that Scapharca subcrenata was the main driver of the microbial community's interspecies-interaction (PERMANOVA, R = 0.0572, P = 0.005) in the treatment zone (TZ). Analysis of co-occurrence networks based on random matrix theory (RMT) indicated that the network's complexity parameters were enhanced in the TZ and disrupted in the control zone (CZ) due to eutrophic disturbances. Concurrently, the TZ was correlated with more profound network modifications (i.e., higher modularity, total nodes (n), cohesion, and proportion of positive links), suggesting that S. subcrenata influenced microbial interspecies interactions in the system. Similarly, the co-occurring networks of generalists Proteobacteria (OTU2037) at genus Anaerospora and Actinobacteria (OTU9660) at genus Candidatus aquiluna for anaerobic ammonia-oxidation (ANAMMOX) were highly significant in the TZ. The top-down and bottom-up forces of S. subcrenata influenced the removal efficiency of nitrogenous compounds by reducing 81.51% of nitrite (NO₂^--N), 84.61% of total ammonium nitrogen (TAN) and 72.78% of nitrate (NO₃^--N). Generally, the introduction of ark shell bivalve (S. subcrenata) to the system as a biofilter provides a very low-cost bioremediation technology that could be one of the best restorations and remediation tools for mariculture effluents.

Decay and persistence of empty bivalve shells in a temperate riverine system

Bivalve shells can persist over a geological time, acting as important physical resources to the associated fauna. However, few studies have investigated their relevance as persistent long-term ecological attributes to the ecosystem. As such, it is relevant to investigate the shell decays in riverine systems subjected to different environmental conditions. Towards this end, shells of four bivalve species (Anodonta anatina, Corbicula fluminea, Potomida littoralis and Unio delphinus) were made available individually and in clusters of different sizes. The effects of river flow and seasonality were assessed by recording the decay rates of shells in lentic and lotic habitats throughout the year. Our results evidenced that the decays varied among species and depend on shell size, water flow and season. Thin shelled species (A. anatina and U. delphinus) showed the highest mean percentage of decay per month, 3.17% (lotic) and 2.77% (lotic), respectively, and thick shelled species (C. fluminea and P. littoralis) the lowest, 2.02% (lotic) and 1.83% (lotic), respectively. Size was a relevant variable explaining decays, with the smallest shells presenting the highest values, 1.2-2.0 times higher compared to the other size classes. Also, robustness showed to be the most relevant feature explaining the decays in thick shelled species. River flow was also a relevant descriptor of the decays, with higher decays observed in the lotic compared to the lentic habitats. Furthermore, lower decays were observed mainly during summer (lentic site), and autumn (lotic site) associated to the burial effect of leaves. In summary, shells of the native species A. anatina and U. delphinus are expected to persist and contribute less as habitat engineering species, than shells of the native P. littoralis and invasive C. fluminea species. This is especially valid to lotic habitats where the decays were up to 2.13 times higher than in lentic habitats.

Non-native freshwater fauna in Portugal: A review

We present the most updated list of non-native freshwater fauna established in Portugal, including the Azores and Madeira archipelagos. This list includes 67 species at national level but corresponds to 84 species records, of which 53 are in the mainland, 23 in the Azores and 8 in Madeira archipelagos. We also discuss the progression of the cumulative number of introductions since 1800 and identify the most probable vectors of introduction, main taxonomic groups and their regions of origin. Furthermore, we review the existing knowledge about ecological and economic impacts, invasion risk and potential distribution of invaders, under present and future climatic conditions, and the applied management actions, including the production of legislation. Along the 20th century the number of successful introductions increased at an approximate rate of two new species per decade until the beginning of 1970s. Since then, this rate increased to about 14 new species per decade. These introductions were mainly a result of fisheries, as contaminants or for ornamental purposes. Fish and mollusks are the taxonomic groups with more established species, representing more than half of the total. Most species (>70%) are native from other regions of Europe and North America. Studies about ecological or socioeconomic impacts are more common for fish, crustaceans and mollusks. Impacts for most amphibians, reptiles and mammals are not thoroughly studied. A few studies on the impacts and management actions of health-threatening mosquitoes are also available. The potential distribution in the Portuguese territory was modelled for 26 species. Only a minority of these models provides projections of distributions under scenarios of future climate change. A comparison of the Portuguese and EU legislation shows large discrepancies in the invasive species lists. Using the EU list and a ranking procedure for the national context, we identify freshwater species of high national concern for which actions are urgently needed.

Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves

Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.

Bioturbation by the razor clam (Sinonovacula constricta) on the microbial community and enzymatic activities in the sediment of an ecological aquaculture wastewater treatment system

Bioturbation by the razor clam, Sinonovacula constricta, influenced the redox conditions and changed the sedimentary environment, providing a suitable micro-environment for microbial growth. However, the mechanism of the integrated razor clam-microbial community in organic matter mineralization remains elusive. To study this mechanism, an in situ experiment was conducted to investigate the bioturbation effects of S. constricta on the microbial community and enzyme activities in the sediment of an ecological aquaculture wastewater treatment system. According to principal coordinate analysis (PCoA) and PERMANOVA, we found that the microbial community was significantly (P < 0.05) influenced by the bioturbation effect of S. constricta. Linear discriminant analysis effect size (LEfSe) showed that species involved in reduced effluent concentrations of TN and TP, such as Prolixibacteraceae, Nitrospira and Actinobacteria, were increased significantly (P < 0.05) by S. constricta. Molecular ecological network (MENs) analysis indicated that the bioturbation effect of S. constricta increased the complexity of interspecies interaction and changed the topological properties of individual OTUs. The results elucidated that S. constricta increased the microbial community network, as substantiated by a higher total number of nodes and a shorter geodesic distance. Zi < 2.5 and Pi <0.62 in MENs showed that the S. constricta treatment significantly increased (P < 0.05) the potential microbial community, with the keystone (OTU747049) Proteobacteria and (OTU74388) Bacteroidetes family Prolixibacteraceae, which connected different co-expressed OTUs. Furthermore, S. constricta significantly increased (P < 0.05) the enzymatic activities (alkaline phosphatase (APA), dehydrogenase and urease) of the substrate at different sampling depths. Overall, this study provides evidence that the bioturbation effect of S. constricta changes the microbial community structure, increases enzymatic activities and accelerates the degradation of organic matter in an aquaculture wastewater environment.

Assessing the effects of temperature and salinity oscillations on a key mesopredator fish from European coastal systems

A population dynamics model was developed to assess the short and long-term effects of temperature and salinity variations in the common goby Pomatoschistus microps in a Portuguese estuary (Minho estuary, NW Portugal). The population was divided into juveniles, females and males, which constituted the model's state variables. Linear regressions between the observed and the predicted density of juveniles, females and the total population were significant. Parameter's sensitivity and uncertainty analysis were estimated. The model was able to satisfactory describe the P. microps population dynamics, and thus was used to simulate the effects of climatic changes on the fish population. Simulations indicated that the common goby population is sensitive to both temperature and salinity changes. Overall, scenarios of more than 3 °C increase caused significant population decreases. Similarly, increased salinities led to a population shrinkage, whereas scenarios of salinity decrease generated an opposite variation on the population. According to the IPCC predictions for climatic tendencies, the population of the common goby will tend to decrease in the near future, experiencing marked oscillations (decrease or increase) during climatic extremes, namely droughts and floods, respectively. These results may be a useful for future planning and management of estuarine systems given that the common goby is an important species of estuarine food webs in many temperate ecosystems.

Environmentally applications of invasive bivalves for water and wastewater decontamination

The environmental and economic impact of invasive bivalve species implies the development of suitable pest management strategies. Chemical control is the most usual approach. However, the production of toxic intermediates as well as the unavoidable impact over non target biota is of special concern. Another approach consists on the physical removal of the animals from the invaded sites. The high biofiltration and bioaccumulation capacity of such animals make them interesting for the removal of contaminants from water and wastewater. In this context, environmental applications can be given for these pests encompassing nutrients removal for the recovery of eutrophic sites, water disinfection, organic and metal contaminants abatement. These approaches may be integrated with pest management where the physical removed animals from the invaded spots could be used for assembling biofilter for water and wastewater decontamination. However, some drawbacks must be addressed before proposing such alternative. In fact, the further spreading of the bivalves into non-invaded sites must be avoided. Moreover, some operational questions must be addressed such as the fate of contaminated animals after biofiltration. Bearing in mind the interesting results already available in this subject, this paper aims to critically overview literature regarding the environmental applications of invasive bivalves.

Effect of freshwater mussels on the vertical distribution of anaerobic ammonia oxidizers and other nitrogen-transforming microorganisms in upper Mississippi river sediment

Targeted qPCR and non-targeted amplicon sequencing of 16S rRNA genes within sediment layers identified the anaerobic ammonium oxidation (anammox) niche and characterized microbial community changes attributable to freshwater mussels. Anammox bacteria were normally distributed (Shapiro-Wilk normality test, W-statistic =0.954, p = 0.773) between 1 and 15 cm depth and were increased by a factor of 2.2 (p < 0.001) at 3 cm below the water-sediment interface when mussels were present. Amplicon sequencing of sediment at depths relevant to mussel burrowing (3 and 5 cm) showed that mussel presence reduced observed species richness (p = 0.005), Chao1 diversity (p = 0.005), and Shannon diversity (p < 0.001), with more pronounced decreases at 5 cm depth. A non-metric, multidimensional scaling model showed that intersample microbial species diversity varied as a function of mussel presence, indicating that sediment below mussels harbored distinct microbial communities. Mussel presence corresponded with a 4-fold decrease in a majority of operational taxonomic units (OTUs) classified in the phyla Gemmatimonadetes, Actinobacteria, Acidobacteria, Plantomycetes, Chloroflexi, Firmicutes, Crenarcheota, and Verrucomicrobia. 38 OTUs in the phylum Nitrospirae were differentially abundant (p < 0.001) with mussels, resulting in an overall increase from 25% to 35%. Nitrogen (N)-cycle OTUs significantly impacted by mussels belonged to anammmox genus Candidatus Brocadia, ammonium oxidizing bacteria family Nitrosomonadaceae, ammonium oxidizing archaea genus Candidatus Nitrososphaera, nitrite oxidizing bacteria in genus Nitrospira, and nitrate- and nitrite-dependent anaerobic methane oxidizing organisms in the archaeal family “ANME-2d” and bacterial phylum “NC10”, respectively. Nitrosomonadaceae (0.9-fold (p < 0.001)) increased with mussels, while NC10 (2.1-fold (p < 0.001)), ANME-2d (1.8-fold (p < 0.001)), and Candidatus Nitrososphaera (1.5-fold (p < 0.001)) decreased with mussels. Co-occurrence of 2-fold increases in Candidatus Brocadia and Nitrospira in shallow sediments suggests that mussels may enhance microbial niches at the interface of oxic–anoxic conditions, presumably through biodeposition and burrowing. Furthermore, it is likely that the niches of Candidatus Nitrososphaera and nitrite- and nitrate-dependent anaerobic methane oxidizers were suppressed by mussel biodeposition and sediment aeration, as these phylotypes require low ammonium concentrations and anoxic conditions, respectively. As far as we know, this is the first study to characterize freshwater mussel impacts on microbial diversity and the vertical distribution of N-cycle microorganisms in upper Mississippi river sediment. These findings advance our understanding of ecosystem services provided by mussels and their impact on aquatic biogeochemical N-cycling.