Water Microbiota Research Articles

With global warming, the aquaculture industry faces many challenges, especially temperature stress, as rising and fluctuating temperatures disrupt aquatic organisms' metabolism, threatening the industry's sustainability. The utilization of probiotics offers a viable solution for dealing with these concerns. This study aimed to explore and evaluate a newly discovered Lactococcus strain as a potential candidate for probiotic application to mitigate the adverse effects of high temperature. Our results showed that the strain of L. lactis L103, displayed promising probiotic attributes. Specifically, it augmented both the weight gain rate and the specific growth rate of Alosa sapidissima. Additionally, a restructuring took place in the intestinal microbial makeup. The relative proportion of beneficial bacteria like Lactococcus and Bacillus increased, while that of the pathogenic Vibrio decreased. The findings from the correlation analysis of environmental elements indicated that TP exerted the most significant influence on the water microbial community. TN was positively correlated with the potentially dominant intestinal bacteria Lactococcus. By modifying the levels of TP and [Formula: see text]-N in water, dietary probiotics were able to exert a particular influence on the microbial community structures both in the aquatic environment and within the intestines of American shad. In conclusion, L. lactis L103 exhibits excellent probiotic potential for juvenile A. sapidissima aquaculture under high-temperature conditions. It promoted fish growth, optimized intestinal microbiota, and regulated the aquatic microbial environment by influencing key nutrient factors (TP, TN). This study provided direct experimental evidence for applying L. lactis L103 as a targeted probiotic to mitigate high-temperature stress in A. sapidissima farming, while offering a practical microbial regulation strategy to enhance the sustainability of this aquaculture sector amid global warming.

Amphibian skin is integral to promoting normal physiological processes in the body and promotes both innate and adaptive immunity against pathogens. The amphibian skin microbiota is comprised of a complex assemblage of microbes and is shaped by internal host characteristics and external influences. Skin disease is a significant source of morbidity and mortality in amphibians, and increasing research has shown that the amphibian skin microbiota is an important component in host health. The Eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a giant salamander declining in many parts of its range, and captive-rearing programs are important to hellbender recovery efforts. Survival rates of juvenile hellbenders in captive-rearing programs are highly variable, and mortality rates are overall poorly understood. Deceased juvenile hellbenders often present with low body condition and skin abnormalities. To investigate potential links between the skin microbiota and body condition, we collected skin swab samples from 116 juvenile hellbenders and water samples from two holding tanks in a captive-rearing program. We used 16s rRNA gene sequencing to characterize the skin and water microbiota and observed significant differences in the skin microbiota by weight class and tank. The skin microbiota of hellbenders that were housed in tanks in close proximity were generally more similar than those housed physically distant. A single taxa, Parcubacteria, was differentially abundant by weight class only and observed in higher abundance in low weight hellbenders. These results suggest a specific association between this taxa and Low weight hellbenders. Additional research is needed to investigate how husbandry factors and potential pathogenic organisms, such as Parcubacteria, impact the skin microbiota of hellbenders and ultimately morbidity and mortality in the species.

Amphibian skin is integral to promoting normal physiological processes in the body and promotes both innate and adaptive immunity against pathogens. The amphibian skin microbiota is comprised of a complex assemblage of microbes and is shaped by internal host characteristics and external influences. Skin disease is a significant source of morbidity and mortality in amphibians, and increasing research has shown that the amphibian skin microbiota is an important component in host health. The Eastern hellbender (Cryptobranchus alleganiensis alleganiensis) is a giant salamander declining in many parts of its range, and captive-rearing programs are important to hellbender recovery efforts. Survival rates of juvenile hellbenders in captive-rearing programs are highly variable, and mortality rates are overall poorly understood. Deceased juvenile hellbenders often present with low body condition and skin abnormalities. To investigate potential links between the skin microbiota and body condition, we collected skin swab samples from 116 juvenile hellbenders and water samples from two holding tanks in a captive-rearing program. We used 16s rRNA gene sequencing to characterize the skin and water microbiota and observed significant differences in the skin microbiota by weight class and tank. The skin microbiota of hellbenders that were housed in tanks in close proximity were generally more similar than those housed physically distant. A single taxa, Parcubacteria, was differentially abundant by weight class only and observed in higher abundance in low weight hellbenders. These results suggest a specific association between this taxa and Low weight hellbenders. Additional research is needed to investigate how husbandry factors and potential pathogenic organisms, such as Parcubacteria, impact the skin microbiota of hellbenders and ultimately morbidity and mortality in the species.

Antibiotic resistance genes in multi-matrices of Chaohu Lake: Spatiotemporal variation and correlation with pesticides and PPCPs.

IntroductionEmerging contaminants such as microplastics (MPs) and antibiotics pose increasing environmental and public health risks due to their persistence and incomplete removal by wastewater treatment processes. MPs can act as vectors for antibiotics, facilitating their environmental spreading and supporting biofilm formation, which can enhance horizontal gene transfer and antibiotic resistance. This study investigates the combined effects of ciprofloxacin (CIP) and polyethylene terephthalate (PET) MPs on microbiota in alpine spring water (SW) sourced from a rock glacier.MethodsFour experimental scenarios (Control, CIP, PET, CIP + PET) were established to assess the sorption dynamics of CIP onto PET particles and the consequent microbial responses. A multidisciplinary analytical approach combining ultra-performance liquid chromatography, microscopy, quantitative PCR, and metabarcoding was applied.ResultsCIP exhibited progressive sorption onto PET, accompanied by a time-dependent increase in biofilm formation, most pronounced in the CIP + PET condition. qPCR revealed elevated copy numbers of resistance genes qnrA and qnrB in CIP + PET, suggesting synergistic effects between antibiotics and MPs in promoting resistance. CIP was the dominant driver of microbial compositional shifts, favoring known CIP-degrading taxa. A shared core microbiome of 216 amplicon sequence variants was detected across all conditions, but specific taxa were differentially enriched under varying exposures. The combined CIP + PET test induced the strongest community shifts, while CIP alone shared fewer taxa with controls, indicating selective pressure for resistant microorganisms like Achromobacter. PET MPs also shaped distinct microbial assemblages, possibly by offering niches favoring biofilm-associated genera such as Luteolibacter. Biodiversity metrics showed highest richness and evenness in CIP-free conditions (Control and PET), while CIP significantly reduced alpha diversity, favoring resistant taxa, as confirmed by NMDS and lower Shannon and Simpson indices. Effects of MPs were still noticeable.ConclusionThese findings demonstrate the disruptive effects of CIP on alpine freshwater microbial communities and highlight the additional, though more moderate, influence of MPs. The combined presence of MPs and antibiotics may exacerbate resistance spreading by enhancing persistence and providing favorable conditions for resistant biofilms. A mechanistic understanding of these interactions is essential for accurate risk assessment and the development of effective mitigation strategies in alpine and other vulnerable freshwater ecosystems.

BackgroundEnvironmental microbiomes, such as those in recirculating aquaculture systems (RAS), can play a key role in shaping host-associated microbial communities. In zebrafish (Danio rerio) research, these interactions can introduce uncontrolled sources of variation, potentially confounding experimental outcomes across multiple facilities. Despite widespread zebrafish use in microbiome studies, few have characterized the microbial composition of both tank water and fish across multiple independent facilities to evaluate the consequences of environmental microbiome variation on the host microbiome.ResultsWe compared water and zebrafish gut microbiomes across five aquaculture facilities—two in the United States and three in Norway—using a nested sampling design and 16S rRNA gene sequencing. Alpha diversity was consistently higher in tank water than in fish guts, and beta diversity metrics revealed distinct clustering by sample type, facility, and location. Differences in microbial community composition were significant across facilities, with both water and fish samples exhibiting facility-specific profiles. Similarity Percentage analysis identified taxonomic groups driving these differences, while Fast Expectation-Maximization for Microbial Source Tracking detected measurable contributions of tank water microbiota to zebrafish gut communities. Bray-Curtis dissimilarity values were lowest between fish and water from the same tank and increased with geographic and facility distance, indicating local microbial overlap. Relative abundance patterns and ordination plots further supported distinct and structured microbial assemblages across systems.ConclusionsThis study demonstrates that zebrafish aquaculture systems harbor unique microbial communities shaped by both environmental and geographic factors, with tank water acting as a potential source of gut-associated microbes. These findings underscore the importance of incorporating environmental microbiome assessments into zebrafish experimental design, particularly for studies focused on host-microbe interactions. Without such consideration, unaccounted variation in environmental microbiota may affect microbiome composition and reduce cross-study reproducibility. Moving forward, standardized reporting of environmental conditions and microbial composition across facilities will be critical for strengthening reproducibility and interpretation in zebrafish microbiome research.

The lotus-fish co-culture (LFC) system leverages plant-fish symbiosis to optimize aqua-culture environments, enhancing both economic and ecological yields. However, the eco-logical mechanisms of microbial communities in LFC systems remain poorly understood, particularly regarding the functional roles of fungi, archaea, and viruses. This study compared microbiota (viruses, archaea, fungi) in water, sediment, and fish (crucian carp) gut of LFC and intensive pond culture (IPC) systems using integrated metagenomic and environmental analyses. Results demonstrated that LFC significantly reduced concentrations of total nitrogen, total phosphorus, and nitrite nitrogen and chemical oxygen demand in water, and organic matter and total nitrogen in sediment compared to IPC. Community diversity analysis, LefSe, and KEGG annotation revealed suppressed viral diversity in LFC, yet increased complexity and stability of intestinal virus communities compared to IPC. Archaeal and functional analyses revealed significantly enhanced ammonia oxidation and OM decomposition in LFC versus IPC, promoting methane metabolism equilibrium and sediment organic matter decomposition. Moreover, crucian carp intestines in LFC harbored abundant Methanobacteria, which contributed to maintaining a low hydrogen partial pressure, suppressing facultative anaerobes and reducing intestinal infection risk. The abundance of fungi in sediment and crucian carp intestine in LFC was significantly higher than that in IPC, showing higher ecological self-purification ability and sustainability potential in LFC. Collectively, LFC's optimized archaeal-fungal networks strengthened host immunity and environmental resilience, while viral community suppression reduced pathogen risks. These findings elucidate microbiome-driven mechanisms underlying LFC's ecological advantages, providing a framework for designing sustainable aquaculture systems through microbial community modulation.

Comparative analysis of the microbiota in wild mud crab (Scylla serrata) intestine, sediment, and water in Koggala Lagoon, Sri Lanka

The black-spotted frog (Pelophylax nigromaculatus) is a common economic species in the rice–frog ecological cropping mode. The present study investigated microbial community structures in paddy water and black-spotted frog’s guts across rice monoculture and low-/high-density rice–frog co-cropping systems at four rice growth stages. Proteobacteria dominate in paddy water, while frog guts are enriched in Firmicutes and Actinobacteriota. The frog density shows no impact on the α-diversity, but rice growth stages significantly alter the Shannon, Simpson, and Pielou_e indices (p < 0.01). Co-cropping may promote amino acid synthesis, elemental cycling, and stress tolerance in paddy water microbiota, which are more diverse than gut microbiota. Strong correlations exist between paddy water and gut microbiotas, with Limnohabitans being linked to gut diversity (p < 0.05). Low-density co-cropping enhances Xenorhabdus, which is beneficial for pest control and stabilizes gut microbiota. The results of this study offer insights for managing rice–frog systems based on rice growth stages.

This study investigated the seasonal and spatial dynamics of off-flavour compounds-geosmin and 2-methylisoborneol (2-MIB)-in an intensive rainbow trout (Oncorhynchus mykiss) aquaculture system for human consumption in western Spain. Weekly water and fish flesh samples were collected over a 12-month period from three farms supplied by the River Tormes. Physicochemical parameters, determination of geosmin and 2-MIB by SPME-GC-MS, microbial counts, and microbial community composition were assessed alongside volatile compound concentrations. Geosmin and 2-MIB showed marked seasonal variation, with peak levels in water and fish flesh during spring and summer, correlating positively with temperature. Geosmin accumulation in fish was highest in the downstream farm, suggesting cumulative exposure effects. In contrast, 2-MIB was detected only in water and at lower concentrations. Microbial analyses revealed high bacterial and fungal diversity, including cyanobacterial taxa such as Phormidium setchellianum and Pseudoanabaena minima, known producers of geosmin and 2-MIB. These findings highlight the importance of water microbiota and environmental conditions in off-flavour development. Managing cyanobacterial populations and monitoring spatial-temporal variability are essential to mitigate the development of earthy or musty flavours and economic losses in aquaculture systems.

Antimicrobial silver materials for drinking water disinfection have become increasingly popular in building-wide systems (e.g., copper-silver ionization) and point-of-use applications (e.g., silver containing plumbing fixtures) to combat the microbial growth of drinking water associated pathogens that can cause infections in the immunocompromised (DWPIs). However, evaluations of various silver-containing treatments suggest that their efficacy is often temporary or incomplete. A potential explanation of these observations is insufficient dosing of silver into the drinking water to reduce these types of microorganisms, which are known to be more resistant to biocides. Instead, sublethal exposure may cause these microorganisms to adapt in ways that increase their resistance to disinfection. In this study, we assessed the effects of different silver concentrations on biofilms of clinically and environmentally isolated Mycobacterium abscessus, a biofilm-forming member of the drinking water microbiota with public health and environmental significance, in a bench-scale system operated to simulated the use patterns of antimicrobial showerheads. We found that high concentrations of silver significantly reduced biofilms cell densities and impacted cellular aggregation behavior, but ultimately made the resulting treated water non-potable due to the concentration of silver needed to solicit these effects. Silver concentrations that were more appropriate for drinking water applications resulting in limited reduction in viable M. abscessus. Additionally, transcriptomic analysis revealed that genes related to stress survival were upregulated in all experimental conditions: genes related to flavoprotein, chaperone, and protease synthesis, ribosome synthesis, and cysteine and methionine metabolism were upregulated in the lower dose condition, and peptidoglycan synthesis and antioxidant production were upregulated in the higher silver dose condition. These expressional changes may enhance survival and pathogenicity traits in M. abscessus after silver exposure. Overall, our findings indicate that silver exposure drives meaningful changes in biofilm behavior and gene expression in M. abscessus isolates, yet does not inactivate M. abscessus under the simulated conditions.

Plant roots play myriad roles that include foraging for resources in complex soil environments. Within this highly dynamic soil environment roots must sense, interact with, and acclimate to factors such as water availability, microbiota, and heterogeneous distribution of nutrients. To aid their acclimation, roots alter their growth and development to optimize their architecture and actively regulate the physical, chemical, and biological properties of their rhizosphere. Understanding the complex interactions between roots and rhizosphere is critical for designing future crops with improved root traits better adapted to diverse and challenging soil conditions. However, studying roots and their interactions with soil under real-world conditions presents significant challenges. Addressing these challenges demands developing realistic laboratory-based model systems and innovative field-based root imaging techniques. Our review surveys the current knowledge and recent advances in understanding root-environment interactions while proposing future solutions to study roots under more "real-life" soil conditions.

Influence of aquaculture practices on microbiota composition and pathogen abundance in pond ecosystems in South China.

Influence of aquaculture pond water microbiota on wound healing in largemouth bass (Micropterus salmoides) via modulation of skin and wound microbiota

To support the sustainable development of rice and aquaculture industries, various rice-animal coculture systems have been developed. One such system, the rice-crab coculture system (RCC), has been practiced for decades in northern China. However, studies on the crab physiological status in RCC remain limited. Microorganisms play a crucial role in aquaculture by influencing animal nutrition, health, nutrient cycling, water quality, and environmental impact. Research on the gut and environmental microbiota in RCC is scarce. This study compared the growth performance, immune and digestive enzyme activities of crabs between RCC and traditional pond farming system (PF). In addition, the microbiota in crab guts, water, and sediment from both systems was investigated using 16S rRNA gene sequencing. Crabs in RCC exhibited superior growth performance and higher enzymatic activities, including acid phosphatase (ACP), alkaline phosphatase (AKP), lipase (LPS), and trypsin (TRY). Significant differences were observed in microbiota composition across crab gut, water, and sediment samples, respectively. RCC crabs had a lower abundance of Bacteroidota and a higher abundance of Firmicutes in their gut microbiota. The RCC environment was enriched with beneficial bacteria such as Rhizobiales, Methylococcales, KD4-96, C39, Xanthomonadales, and Nitrosomonadaceae. Microbial function predictions confirmed enhanced methanotrophy and nitrogen fixation in the RCC. The RCC enhances the growth rate and immune capability of crabs. Crabs from RCC consume more animal-based nutrition, which results in distinct differences in gut microbiota composition and higher levels of LPS and TRY compared to those in PF. Additionally, RCC supports environmentally beneficial bacteria that contribute to greenhouse gas reduction, carbon and nitrogen fixation, organic matter decomposition, and ammonia oxidation, benefiting both the crabs and their ecosystem. These findings enhance our understanding of crab physiology and microbial communities in RCC and PF systems.

This article reviews the scientific literature discussing the microbial interactions between water microbiota, live food microbiota, fish larvae immune system and gut microbiota, and biofilm microbial communities in rearing systems for marine fish larvae. Fish gut microbiota is the first line of defense against opportunistic pathogens, and marine fish larvae are vulnerable to high mortalities during the first weeks after hatching. The bacterial colonization of fish larvae is a dynamic process influenced by environmental and host-related factors. The bacteria transferred to larvae from the eggs can influence the composition of the gut microbiota in the early stages of fish. Fish larvae ingest free-living microorganisms present in the water, as marine fish larvae drink water for osmoregulation. In marine aquaculture systems, the conventional feeding-rearing protocol consists of zooplankton (rotifers, Artemia, and copepods). These live food organisms are filter-feeders. Once transferred to a new environment, they quickly adopt the microflora of the surrounding water. So, the water microbiota is similar to the microbiota of the live food at the time of ingestion of live food by the larvae. In aquaculture rearing systems, bacterial biofilms may harbor opportunistic pathogenic bacteria and serve as a reservoir for those microbes, which may colonize the water column. The methods applied for the study of fish larvae microbiota were reviewed.

To understand better the high microbial load in dried laver (Porphyra yezoensis or nori), this study analyzed the aerobic plate count (APC), coliform count, temperature change, and microbiota of processing water, laver materials, and food contact surface (FCS) samples from three processing plants during the dried laver processing season from December 2023 to April 2024. The seawater used for the first washing had a low microbial load (APCs < 1-2.85 log CFU/g; coliform < 1 log CFU/g) and was dominated by Proteobacteria, Firmicutes, and Bacteroidota. The microbial load of fresh laver (4.21-4.76 log CFU/g) remained unchanged after seawater washing, but significantly increased after continuous shredding, sponge dehydration, first drying, and with the seasonal temperature rise. The microbiota of laver before drying was vulnerable between processing steps and seasons, but consistently shifted back to fresh laver microflora and was dominated by Flavobacteriaceae after drying. The FCSs (except for the curtain), which had a high microbial load (APCs 5.25-8.26 log CFU/g; coliform 1.52-4.84 log CFU/g) with similar microbiota to seawater, caused the secondary contamination of laver during processing. This study revealed the microbial proliferation of laver and seawater microflora in the continuous processing line with high nutrients and with the seasonal processing water temperature rise caused by the local weather, highlighting the need for routine cleaning and sanitizing, better washing of fresh laver, and low temperature control for future dried laver production.

BackgroundZostera marina is an important ecosystem engineer influencing shallow water environments and possibly shaping the microbiota in surrounding sediments and water. Z. marina is typically found in marine systems, but it can also proliferate under brackish conditions. Changes in salinity generally have a strong impact on the biota, especially at the salty divide between salinity 6 and 9. To better understand the impact of the salty divide on the interaction between Z. marina and the surrounding sediment and water microbiota, we investigated the effects of Z. marina meadows on the surrounding microbiota across a salinity range of 6–15 in the Baltic Sea during the summer using 16S and 18S rRNA gene amplicon sequencing.ResultsSalinity was the most important factor for structuring the microbiota within both water and sediment. The presence of Z. marina affected the composition of the bacterial and eukaryotic community and bacterial alpha diversity in the sediment. However, this effect was confined to alpha-mesohaline conditions (salinity 9–15). The impact of Z. marina below salinity 9 on water and sediment microbiota was insignificant.ConclusionsIncreasing salinity was associated with a longer leaf length of Z. marina, causing an increased canopy height, which affects the sediment microbiota through reduced water velocity. Hence, we propose that the canopy effect may be the major predictor explaining Z. marina’s interactions with the surrounding microbiota at salinity 9–15. These findings emphasize the importance of the physical effects of Z. marina meadow ecosystem services and have important implications for Z. marina management under brackish conditions in a changing climate.

The salt lake ecosystem, characterized by extreme environmental gradients, harbors microbes that uniquely adapt to high salt stress through natural selection. However, how abiotic and biotic factors shape the microbial community assembly in Yuncheng Salt Lakes remains unclear. Here, we investigated the assembly processes and meta co-occurrence patterns of microbiota in both water and sediment sampled from 14 distinct wide range of salinity lakes in the Shanxi Yuncheng area, Midwest of China, using 16S rRNA and 18S rRNA gene sequencing technology combined with multivariate ecological and statistical methods. Habitat differentiation led to the differences in microbial diversity, co-occurrence patterns, and community assembly between sedimentary and planktonic communities. Sedimentary prokaryotes were more shaped by deterministic processes than planktonic bacterial communities. Salinity was a major abiotic factor influencing the balance between stochastic and deterministic processes in both sediment and water. Enhanced microbial interactions within sediments exhibited a more prominent impact in shaping community assembly, as indicated by the stronger association between network-inferred species and prokaryotic βNTI. Moreover, we revealed significant differences in how core species concerning βNTI responded to biotic and abiotic factors. Our findings elucidated the ecological process underlying microbial communities in Yuncheng Salt Lakes and shed light on the mechanism of microorganisms to maintain community complexity and diversity in the extreme environment.Key points• Sedimentary prokaryotes were more shaped by deterministic processes than planktonic prokaryotic communities.• Salinity was a major factor influencing the balance between stochastic and deterministic process.• Inter-domain and intra-domain symbiotic interactions within sedimentary communities represent key biotic factors influencing their community assembly.Graphical abstract

Artemia franciscana farmed in Vinh Chau, Vietnam, have been known for their premium‐quality cysts. This study provides an update on Artemia cyst production in solar earthen ponds in Vinh Chau and explores the microbiome of Artemia gut, pond water, and pond sediment in order to generate clues for research on cyst productivity improvement. We monitored cyst productivity of two pond groups as follows: a more productive one (HIGHER) and a less productive one (LOWER); and conducted two samplings, one mid‐crop and the other at the end for microbiome analyses. Cyst productivity averaged at 112.0 ± 22.3 kg/ha/crop with large variation among the studied ponds. The HIGHER group produced 160.6 ± 10.3 kg/ha/crop or 2.5 folds significantly higher than that by the LOWER group (63.2 ± 18.7 kg/ha/crop) (p &lt; 0.05). Higher feeding rate and fertilization rate were strongly associated with higher cyst productivity (p &lt; 0.05). The microbiota of Artemia gut had the lowest diversity compared with pond water and pond sediment. Microalgae, such as diatoms and Dunaliella, halophilic bacteria (Halomonas spp), and Vibrio were the dominant taxa in Artemia gut. Their relative abundances changed over time as the result of increasing salinity and extreme water temperatures. Fungi were present in Artemia gut and pond sediment but did not appear to be important to Artemia. Bacterial communities were very different among Artemia gut, pond water, and pond sediment. The highest diversity was recorded for pond sediment, followed by pond water and Artemia gut. Ponds with higher cyst productivity tended to have higher bacterial diversity in pond sediment. More significant temporal variations were found with the bacterial communities of pond water compared with pond sediment and Artemia gut. Overall, the observed differences in microbiota of Artemia gut, pond water, and pond sediment between the two pond groups (or cyst productivity levels) emphasized the importance of microalgae as the major food source, interesting roles of Vibrio and pond management.