High spatial heterogeneity and low connectivity of bacterial communities along a Mediterranean subterranean estuary

Genome-centric metagenomes unveiling the hidden resistome in an anchialine cave

BACKGROUND

Antibiotic resistance is a critical global concern, posing significant challenges to human health and medical treatments. Studying antibiotic resistance genes (ARGs) is essential not only in clinical settings but also in diverse environmental contexts. However, ARGs in unique environments such as anchialine caves, which connect both fresh and marine water, remain largely unexplored despite their intriguing ecological characteristics.

RESULTS

We present the first study that comprehensively explores the occurrence and distribution of ARGs and mobile genetic elements (MGEs) within an anchialine cave. Utilizing metagenomic sequencing we uncovered a wide array of ARGs with the bacitracin resistance gene, bacA and multidrug resistance genes, being the most dominant. The cave's microbial community and associated resistome were significantly influenced by the salinity gradient. The discovery of novel β-lactamase variants revealed the cave's potential as a reservoir for previously undetected resistance genes. ARGs in the cave demonstrated horizontal transfer potential via plasmids, unveiling ecological implications.

CONCLUSIONS

These findings highlight the need for further exploration of the resistome in unique environments like anchialine caves. The interconnected dynamics of ARGs and MGEs within anchialine caves offer valuable insights into potential reservoirs and mechanisms of antibiotic resistance in natural ecosystems. This study not only advances our fundamental understanding but also highlights the need for a comprehensive approach to address antibiotic resistance in diverse ecological settings.

Comparing the Environmental Influences and Community Assembly of Protist Communities in Two Anthropogenic Coastal Areas

Anthropogenic stresses are intensively affecting the structure and function of microbial communities in coastal ecosystems. Despite being essential components of coastal ecosystems, the environmental influences and assembly processes of protist communities remain largely unknown in areas with severe disturbance. Here, we used 18S rRNA gene high-throughput sequencing to compare the composition, assembly process, and functional structure of the protist communities from the coastal areas of the Northern Yellow Sea (NYS) and the Eastern Bohai Sea (EBS). These two areas are separated by the Liaodong Peninsula and experience different anthropogenic stresses due to varying degrees of urbanization. We detected significant differences between the protist communities of the two areas. Environmental and geographic factors both influenced the composition of protist communities, with environmental factors playing a greater role. The neutral community model indicated that the assembly of protist communities was governed by deterministic processes, with stochastic processes having a stronger influence in the EBS area compared to the NYS area. The phototrophic and consumer communities, influenced by different environmental factors, differed significantly between the two areas. Our results provide insights into the biogeography and assembly of protist communities in estuaries under anthropogenic stresses, which may inform future coastal management.

Microbial-induced MnO2 precipitation in a carbonate coastal aquifer

A study was carried out to identify biogeochemical reactions along a transect of a coastal dolomitic aquifer. In this transect, the physicochemical parameters of the groundwater as well as the microbial composition of samples taken at different depths and salinities were measured. Many of the dissolved ions measured in the groundwater follow a pattern that reflects the distribution of the water masses (fresh, interface and salt) in the aquifer, while others such as Ca and Mg ions deviate from this trend by identifying the zones of maximum dissolution of the carbonate matrix. The concentrations of minor ions, such as Fe and Mn, also follow a singular pattern, with maximum concentrations in the reducing zones of the aquifer and lower values in the oxidizing zones. Precipitates of Mn oxides along with other metals, such as Fe, Ba, Zn and Ni, were observed in the saline zone displaying oxidizing conditions close to the coastline, where a continuous core was recovered. This zone, which is located below the freshwater-seawater mixing zone and features percentages of seawater higher than 80 %, is characterized by the presence of Marinobacter as the predominant genus. These bacteria are also related to the formation of Mn-rich polymetallic oxides in other contexts such as the ocean floor (Wang et al., 2012; Cao et al., 2021). All in all, a biogeochemical reaction model is proposed that describes the formation of these oxides in areas close to the discharge zone of coastal aquifers. To do this, it has been necessary to integrate the results obtained from geochemical, hydrogeological and microbiological information.

Recent Advances in Microbial-Assisted Remediation of Cadmium-Contaminated Soil

Soil contamination with cadmium (Cd) is a severe concern for the developing world due to its non-biodegradability and significant potential to damage the ecosystem and associated services. Industries such as mining, manufacturing, building, etc., rapidly produce a substantial amount of Cd, posing environmental risks. Cd toxicity in crop plants decreases nutrient and water uptake and translocation, increases oxidative damage, interferes with plant metabolism and inhibits plant morphology and physiology. However, various conventional physicochemical approaches are available to remove Cd from the soil, including chemical reduction, immobilization, stabilization and electro-remediation. Nevertheless, these processes are costly and unfriendly to the environment because they require much energy, skilled labor and hazardous chemicals. In contrasting, contaminated soils can be restored by using bioremediation techniques, which use plants alone and in association with different beneficial microbes as cutting-edge approaches. This review covers the bioremediation of soils contaminated with Cd in various new ways. The bioremediation capability of bacteria and fungi alone and in combination with plants are studied and analyzed. Microbes, including bacteria, fungi and algae, are reported to have a high tolerance for metals, having a 98% bioremediation capability. The internal structure of microorganisms, their cell surface characteristics and the surrounding environmental circumstances are all discussed concerning how microbes detoxify metals. Moreover, issues affecting the effectiveness of bioremediation are explored, along with potential difficulties, solutions and prospects.

Ecological differentiation and assembly processes of abundant and rare bacterial subcommunities in karst groundwater

The ecological health of karst groundwater has been of global concern due to increasing anthropogenic activities. Bacteria comprising a few abundant taxa (AT) and plentiful rare taxa (RT) play essential roles in maintaining ecosystem stability, yet limited information is known about their ecological differentiation and assembly processes in karst groundwater. Based on a metabarcoding analysis of 64 groundwater samples from typical karst regions in southwest China, we revealed the environmental drivers, ecological roles, and assembly mechanisms of abundant and rare bacterial communities. We found a relatively high abundance of potential functional groups associated with parasites and pathogens in karst groundwater, which might be linked to the frequent regional anthropogenic activities. Our study confirmed that AT was dominated by Proteobacteria and Campilobacterota, while Patescibacteria and Chloroflexi flourished more in the RT subcommunity. The node-level topological features of the co-occurrence network indicated that AT might share similar niches and play more important roles in maintaining bacterial community stability. RT in karst groundwater was less environmentally constrained and showed a wider environmental threshold response to various environmental factors than AT. Deterministic processes, especially homogeneous selection, tended to be more important in the community assembly of AT, whereas the community assembly of RT was mainly controlled by stochastic processes. This study expanded our knowledge of the karst groundwater microbiome and was of great significance to the assessment of ecological stability and drinking water safety in karst regions.

High spatial heterogeneity and low connectivity of bacterial communities along a Mediterranean subterranean estuary

Subterranean estuaries are biogeochemically active coastal sites resulting from the underground mixing of fresh aquifer groundwater and seawater. In these systems, microbial activity can largely transform the chemical elements that may reach the sea through submarine groundwater discharge (SGD), but little is known about the microorganisms thriving in these land-sea transition zones. We present the first spatially-resolved characterization of the bacterial assemblages along a coastal aquifer in the NW Mediterranean, considering the entire subsurface salinity gradient. Combining bulk heterotrophic activity measurements, flow cytometry, microscopy and 16S rRNA gene sequencing we find large variations in prokaryotic abundances, cell size, activity and diversity at both the horizontal and vertical scales that reflect the pronounced physicochemical gradients. The parts of the transect most influenced by freshwater were characterized by smaller cells and lower prokaryotic abundances and heterotrophic production, but some activity hotspots were found at deep low-oxygen saline groundwater sites enriched in nitrite and ammonium. Diverse, heterogeneous and highly endemic communities dominated by Proteobacteria, Patescibacteria, Desulfobacterota and Bacteroidota were observed throughout the aquifer, pointing to clearly differentiated prokaryotic niches across these transition zones and little microbial connectivity between groundwater and Mediterranean seawater habitats. Finally, experimental manipulations unveiled large increases in community heterotrophic activity driven by fast growth of some rare and site-specific groundwater Proteobacteria. Our results indicate that prokaryotic communities within subterranean estuaries are highly heterogeneous in terms of biomass, activity and diversity, suggesting that their role in transforming nutrients will also vary spatially within these terrestrial-marine transition zones.