Biogeographic distribution, ecotype partitioning and controlling factors of Chloroflexi in the sediments of six hadal trenches of the Pacific Ocean

Enhanced sediment microbial diversity in mangrove forests: Indicators of nutrient status in coastal ecosystems

Coastal ecosystems are increasingly threatened by nutrient imbalances and environmental degradation, which can compromise their stability and productivity. We analyzed the sediment characteristics, microbial community structures, and nutrient cycling across three habitats: mangrove forests, seagrass beds, and bare beaches. The physicochemical properties (including pH, total nitrogen (TN), phosphorus (P), and potassium (K)) of the sediment samples were analyzed, and the microbial diversity was assessed using high-throughput sequencing. Our findings indicated that the organic matter (OM), TN, and cation exchange capacity (CEC) of mangrove sediments were significantly higher than those of seagrass beds and bare beaches. The microbial community in mangroves was positively correlated with OM content and was more complex and stable than that in seagrass beds and bare beaches. MG potentially improved the abundance of k00059 and enzyme 1.1.1.100 in sediment bacteria and further increased sediment TN, OM, and CEC. This study indicates the importance of microbial diversity as a potential indicator of sediment and plant nutrient status, emphasizing the need for conservation efforts to preserve mangrove ecosystems.

Variations in the Bacterial, Fungal, and Protist Communities and Their Interactions Within Sediment Affected by the Benthic Organism, Snail Bellamya purificata

In aquatic benthic environments, benthic organisms have been found to regulate important biogeochemical characteristics and perform key ecosystem functions. To further explore the ecological impact of the snail Bellamya purificata's, presence on the benthic environment, we employed high-throughput sequencing technology to investigate its effects on the bacterial, fungal, and protist communities in sediment and their intrinsic interactions. Our findings revealed that B. purificata's presence significantly enhanced the diversity and evenness of the fungal community while simultaneously decreasing the diversity and richness of the protist community, and it also altered the composition and relative abundance of the dominant phyla across the bacterial, fungal, and protist communities. The snail B. purificata considerably altered the co-occurrence networks of the microbial communities, particularly by enhancing the intrinsic complexity of the protist community and by strengthening the interconnections among the protist, bacterial, and fungal communities. Notably, the proportions of specialists within the sediment bacterial, fungal, and protist communities declined due to the snail B. purificata. Its presence also notably expanded the habitat niche breadth for sediment bacteria and protists. In terms of community assembly, B. purificata shifted the fungal community assembly from being dominated by stochastic processes to being dominated by deterministic processes, whereas the protist community assembly shifted from deterministic processes to being dominated by stochastic processes. The mainly altered ecological processes in the fungal and protist assemblies were drift and homogenizing selection. Additionally, the presence of B. purificata resulted in a notable reduction in the sediment ON level and a significant increase in the ammonia, FA, and EN concentrations. Sediment properties, particularly FA and nitrate, were strongly correlated with microbial communities and were key contributors to changes in microbial community dynamics. These research findings not only broadened our understanding of the ecological impacts of B. purificata on benthic microbial communities but also highlighted its substantial potential in enhancing microbial community stability.

Biotic Interaction Underpins the Assembly Processes of the Bacterial Community Across the Sediment-Water Interface in a Subalpine Lake

The sediment-water interface is the most active region for biogeochemical processes and biological communities in aquatic ecosystems. As the main drivers of biogeochemical cycles, the assembly mechanisms and the distribution characteristics of microbial communities at this boundary remain unclear. This study investigated the microbial communities across the sediment-water interface in a natural subalpine lake in China. The results indicated that the diversity of bacterial communities in middle sediment was significantly higher than that in overlying water and other sediments (p < 0.001). Pearson's correlation analysis indicated that the diversity was significantly influenced by biotic factors (e.g., diversity of fungus, protozoan and alga) and physicochemical parameters (e.g., total carbon, total organic carbon, nitrate, ammonium and pH) (p < 0.01). Null model analysis revealed that the homogeneous selection dominated the assembly of the bacteria community in sediment, whereas the heterogeneous selection dominated that in overlying water. The least squares path analysis showed that interactions between protozoa and bacteria had a greater impact on bacterial community assembly (p < 0.001). Important taxa influence the assembly by regulating biotic interactions. These findings provided a basis for understanding the importance of biotic interactions in maintaining subalpine lakes' ecosystems across the sediment-water interface.

Taxonomic and functional partitioning of Chloroflexota populations under ferruginous conditions at and below the sediment-water interface

The adaptation of the phylum Chloroflexota to various geochemical conditions is thought to have originated in primitive microbial ecosystems, involving hydrogenotrophic energy conservation under ferruginous anoxia. Oligotrophic deep waters displaying anoxic ferruginous conditions, such as those of Lake Towuti, and their sediments may thus constitute a preferential ecological niche for investigating metabolic versatility in modern Chloroflexota. Combining pore water geochemistry, cell counts, sulfate reduction rates, and 16S rRNA genes with in-depth analysis of metagenome-assembled genomes, we show that Chloroflexota benefit from cross-feeding on metabolites derived from canonical respiration chains and fermentation. Detailing their genetic contents, we provide molecular evidence that Anaerolineae have metabolic potential to use unconventional electron acceptors, different cytochromes, and multiple redox metalloproteins to cope with oxygen fluctuations, and thereby effectively colonizing the ferruginous sediment-water interface. In sediments, Dehalococcoidia evolved to be acetogens, scavenging fatty acids, haloacids, and aromatic acids, apparently bypassing specific steps in carbon assimilation pathways to perform energy-conserving secondary fermentations combined with CO2 fixation via the Wood-Ljungdahl pathway. Our study highlights the partitioning of Chloroflexota populations according to alternative electron acceptors and donors available at the sediment-water interface and below. Chloroflexota would have developed analogous primeval features due to oxygen fluctuations in ancient ferruginous ecosystems.

Impact of operational conditions on drinking water biofilm dynamics and coliform invasion potential

Biofilms within drinking water distribution systems serve as a habitat for drinking water microorganisms. However, biofilms can negatively impact drinking water quality by causing water discoloration and deterioration and can be a reservoir for unwanted microorganisms. In this study, we investigated whether indicator organisms for drinking water quality, such as coliforms, can settle in mature drinking water biofilms. Therefore, a biofilm monitor consisting of glass rings was used to grow and sample drinking water biofilms. Two mature drinking water biofilms were characterized by flow cytometry, ATP measurements, confocal laser scanning microscopy, and 16S rRNA sequencing. Biofilms developed under treated chlorinated surface water supply exhibited lower cell densities in comparison with biofilms resulting from treated groundwater. Overall, the phenotypic as well as the genotypic characteristics were significantly different between both biofilms. In addition, the response of the biofilm microbiome and possible biofilm detachment after minor water quality changes were investigated. Limited changes in pH and free chlorine addition, to simulate operational changes that are relevant for practice, were evaluated. It was shown that both biofilms remained resilient. Finally, mature biofilms were prone to invasion of the coliform, Serratia fonticola. After spiking low concentrations (i.e., ±100 cells/100 mL) of the coliform to the corresponding bulk water samples, the coliforms were able to attach and get established within the mature biofilms. These outcomes emphasize the need for continued research on biofilm detachment and its implications for water contamination in distribution networks.

IMPORTANCE

The revelation that even low concentrations of coliforms can infiltrate into mature drinking water biofilms highlights a potential public health concern. Nowadays, the measurement of coliform bacteria is used as an indicator for fecal contamination and to control the effectiveness of disinfection processes and the cleanliness and integrity of distribution systems. In Flanders (Belgium), 533 out of 18,840 measurements exceeded the established norm for the coliform indicator parameter in 2021; however, the source of microbial contamination is mostly unknown. Here, we showed that mature biofilms, are susceptible to invasion of Serratia fonticola. These findings emphasize the importance of understanding and managing biofilms in drinking water distribution systems, not only for their potential to influence water quality, but also for their role in harboring and potentially disseminating pathogens. Further research into biofilm detachment, long-term responses to operational changes, and pathogen persistence within biofilms is crucial to inform strategies for safeguarding drinking water quality.

A unique subseafloor microbiosphere in the Mariana Trench driven by episodic sedimentation

Hadal trenches are characterized by enhanced and infrequent high-rate episodic sedimentation events that likely introduce not only labile organic carbon and key nutrients but also new microbes that significantly alter the subseafloor microbiosphere. Currently, the role of high-rate episodic sedimentation in controlling the composition of the hadal subseafloor microbiosphere is unknown. Here, analyses of carbon isotope composition in a ~ 750 cm long sediment core from the Challenger Deep revealed noncontinuous deposition, with anomalous 14C ages likely caused by seismically driven mass transport and the funneling effect of trench geomorphology. Microbial community composition and diverse enzyme activities in the upper ~ 27 cm differed from those at lower depths, probably due to sudden sediment deposition and differences in redox condition and organic matter availability. At lower depths, microbial population numbers, and composition remained relatively constant, except at some discrete depths with altered enzyme activity and microbial phyla abundance, possibly due to additional sudden sedimentation events of different magnitude. Evidence is provided of a unique role for high-rate episodic sedimentation events in controlling the subsurface microbiosphere in Earth's deepest ocean floor and highlight the need to perform thorough analysis over a large depth range to characterize hadal benthic populations. Such depositional processes are likely crucial in shaping deep-water geochemical environments and thereby the deep subseafloor biosphere.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42995-023-00212-y.

Discrepant assembly processes of prokaryotic communities between the abyssal and hadal sediments in Yap Trench

Abyssal and hadal sediments represent two of the most type ecosystems on Earth and have the potential interactions with geochemistry. However, little is known about the prokaryotic community assembly and the response of prokaryotic communities to metal(loid)s in trench sediments due to the lack of adequate and appropriate samples. In this study, a systematic investigation combined the assembly mechanisms and co-occurrence patterns of prokaryotic communities between the hadal and abyssal sediments across the Yap Trench. The results revealed that the hadal prokaryotes had less species diversity, but more abundant function than the abyssal prokaryotes. The prokaryotic communities in the abyssal sediments had more core taxa than the hadal sediments. Twenty-one biomarkers mostly affiliated with Nitrosopumilaceae were detected using Random-Forests machine learning algorithm. Furthermore, stochasticity was dominant in the prokaryotic community assembly processes of the Yap Trench sediments. Meanwhile, homogeneous selection (32.6%-52.9%) belonging to deterministic processes governed the prokaryotic community assembly in hadal sediments with increasing of sediment depth. In addition to total nitrogen and total organic carbon, more metal(loid)s were significantly correlated with the prokaryotic community in the hadal sediments than that in the abyssal sediments. The hadal prokaryotic communities was most positively related to bismuth (r = 0.31, p < 0.01), followed by calcium, chromium, cerium, potassium, plumbum, scandium, titanium, and vanadium. Finally, co-occurrence networks revealed two potential dominant prokaryotic modules in Yap Trench sediments covaried across oceanographic zonation. By contrast, the hadal network had relatively more complexity, more bacterial taxa, and more associations among prokaryotic taxa, relative to the abyssal network. This study reveals potentially metal variables and community assembly mechanisms of the prokaryotic community in abyssal and hadal sediments and provides a better understanding on the prokaryotic diversity and ecology in trench sediment ecosystems.

Key bacteria decomposing animal and plant detritus in deep sea revealed via long-term in situ incubation in different oceanic areas

Transport of organic matter (OM) occurs widely in the form of animal and plant detritus in global oceans, playing a crucial role in global carbon cycling. While wood- and whale-falls have been extensively studied, the in situ process of OM remineralization by microorganisms remains poorly understood particularly in pelagic regions on a global scale. Here, enrichment experiments with animal tissue or plant detritus were carried out in three deep seas for 4-12 months using the deep-sea in situ incubators. We then performed community composition analyses as well as metagenomic and metatranscriptomic analyses. The results revealed strikingly similar microbial assemblages responsible for decomposing animal and plant detritus. Genes encoding peptidases and glucoside hydrolases were highly abundant and actively transcribed in OM enrichments, which confirmed the roles of these enriched microbial assemblages in organic decomposition. Marinifilaceae, Desulfocapsaceae, Spirochaetaceae, and o-Peptostreptococcales were found to potentially contribute to nitrogen fixation. These core bacteria, acting as cosmopolitan anaerobes in decomposing fast-sinking particulate OM, may have been underestimated in terms of their role in deep-sea microbial-mediated biogeochemical cycles during conventional sampling and diversity survey.