pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments

Pu, Haiguang; Yuan, Youxi; Qin, Lei; Liu, Xiaohui

doi:10.3390/microorganisms11030676

Cited by 9 publications

(2 citation statements)

References 89 publications

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“…Additionally, high levels of plant and microbial diversity act as buffers for grassland ecosystems by decreasing the negative effect of drought on overall biodiversity (Castillioni et al, 2020;Jin et al, 2022). In contrast, lakes may be affected by drought more directly with decreased water levels causing acidification or alkalization (Li et al, 2017), modifying sediment carbon content (Weise et al, 2016), and destabilizing microbial communities (Pu et al, 2023).…”

Section: Introductionmentioning

confidence: 99%

Effects of drought-induced stress on nematode communities in aquatic and terrestrial habitats of the Nebraska Sandhills

Gattoni,

Gendron,

Powers

et al. 2024

Front. Ecol. Evol.

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IntroductionGlobal change events (e.g., worsening drought) are increasing environmental stress in a variety of terrestrial and aquatic habitats. The degree to which communities in soils and sediments are driven by temporal environmental changes across multiple habitat types from the same region is not clear.MethodsWe used nematodes, a common bioindicator of soil and sediment health, to determine how community diversity and composition are altered by rising alkalinity across lakes, shorelines, and prairies in the western Nebraska Sandhills. We sampled these three habitats from five lake basins spanning an alkalinity gradient (pH 7–11) across three years (2019, 2020, 2021). During our sampling, the Sandhills experienced a range of drought intensities, with 2019 being a wet year, followed by severe drought in 2020, and abnormally dry/moderate drought in 2021. To determine if diversity and composition of nematodes responded to increased alkalinity and drought-induced stress we used different modelling approaches, including Random Forest and pairwise comparisons.Results and discussionOverall, nematode diversity in lakes was most affected by increasing alkalinity over time, whereas in shorelines and prairies diversity was most reliant on bacterial diversity and potential nematode-nematode interactions. In comparison to shorelines and prairies, community composition in lakes was the least variable and consistently driven by pH and lake water levels. In contrast, compositions in the shorelines and prairies were more variable and explained at varying degrees by pH, year, lake basin, and climate-associated variables. In addition, relative abundance and compositional nature of select copious taxa were highly unpredictable, indicating potential instability in these habitats. Future research is necessary to address the ecologic stability of the Sandhills and determine where conservation efforts are most needed.

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Section: Introductionmentioning

confidence: 99%

Effects of drought-induced stress on nematode communities in aquatic and terrestrial habitats of the Nebraska Sandhills

Gattoni,

Gendron,

Powers

et al. 2024

Front. Ecol. Evol.

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“…Their variable chemistry provides the opportunity of a "natural experiment" offering a range of characteristics to test which environmental variables influence the taxa profiles and prevalence of antibiotic resistance genes (ARGs). Chemical factors of interest include for example pH (8), tannin levels, nitrates and phosphates (9,10).…”

Section: Introductionmentioning

confidence: 99%

Pond Water Microbiome Taxa Profiles and Antibiotic Resistance Genes Associated with Acidity and Tannins

Vaccaro,

Pilat,

Gusmano

et al. 2024

Preprint

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Microbial communities of small freshwater bodies are poorly understood. Four ponds in Knox County, Ohio, were sampled over two years to investigate the relationship between the microbial taxa profiles, antibiotic resistance genes (ARGs), and environmental factors such as pH and tannin concentrations. For each site, microbial communities were collected by filtration and metagenomes were analyzed by short-read sequencing. Taxa profiles were predicted by the Kraken2/Bracken pipelines. Bacterial taxa with high abundance in these ponds included Betaproteobacteria (Polynucleobacter and Methylopumilus) and Actinobacteria (Planktophila, Nanopelagicus, and Mycolicibacterium). One pond, a former quarry with elevated pH, showed high prevalence of Cyanobacteria with a seasonal shift from Synechococcus to Planktothrix in the fall. Planktothrix increase was associated with acidification. ARGs were quantified using the ShortBRED pipeline to detect and quantify hits to a marker set derived from the Comprehensive Antibiotic Resistance Database (CARD). The top two ARGs with the largest marker hits encode components of a Stenotrophomonas drug efflux pump powered by proton-motive force (smeABC) and a mycobacterial global regulator that activates a drug pump and other cell defenses (mtrA). Pump function and global activation of transcription incur large energy expenditures, whose fitness cost may increase at high external pH where the cell's proton-motive force is diminished. The smeABC and mtrA prevalence showed a modest correlation with acidifying conditions (low pH and high tannins) which contribute a large transmembrane pH difference to the proton-motive force, thus increasing the cell's energy available for pump function and global gene expression. Compared to rivers and lakes, pond microbial ecosystems are understudied despite close contact with agriculture and recreation. Environmental microbes offer health benefits as well as hazards for human contact. Small water bodies may act as reservoirs for drug-resistant organisms and transfer of antibiotic resistance genes. Yet, the public is rarely aware of the potential for exposure to ARG-carrying organisms in recreational water bodies. Little is known about the capacity for freshwater microbial communities to remediate drug pollution and which biochemical factors may select against antibiotic resistance genes. This study analyzes the bacterial taxa composition and ARG prevalence including possible influence of factors such as pH and tannic acid levels.

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Carbon and Nutrient Limitations of Microbial Metabolism in Xingkai Lake, China: Abiotic and Biotic Drivers

Chen,

Zhang,

Geng

et al. 2024

Microb Ecol

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Microbial communities are crucial for water quality and biogeochemical cycling in freshwaters. Microbes secrete extracellular enzymes to decompose organic matter for their needs of nutrients and scarce elements. Yet, there is a lack of knowledge on microbial metabolic limitations in freshwaters, especially in lake sediments. Here, we examined the carbon, nitrogen, and phosphorus-acquiring extracellular enzyme activities and the bacterial and fungal communities of 30 sediments across Xingkai Lake, the largest freshwater lake in Northeast Asia. We further analyzed the microbial metabolic limitations via extracellular enzyme stoichiometry and explored the direct and indirect effects of abiotic and biotic factors on the limitations. We found that microbial metabolisms were primarily limited by phosphorus in Xingkai Lake. For instance, microbial carbon and phosphorus limitations were closely correlated to abiotic factors like water depth, total dissolved solids, sediment total carbon, and conductivity. The metabolic limitations were also affected by biotic factors, such as showing positive relationships with the alpha and beta diversity of bacteria, and with the beta diversity of fungi. In addition, community compositions of bacteria and fungi were mainly correlated to abiotic factors such as total carbon and dissolved organic carbon, respectively. Collectively, microbial metabolic limitations were affected directly or indirectly by abiotic factors and microbial communities. Our findings indicate that microbial metabolic limitations are not only driven by bacteria and fungi but also by abiotic factors such as water depth and total nitrogen, and thus provide empirical evidence for effective management of freshwater lakes under climate warming and intensified human activities.

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pH Drives Differences in Bacterial Community β-Diversity in Hydrologically Connected Lake Sediments

Cited by 9 publications

References 89 publications

Effects of drought-induced stress on nematode communities in aquatic and terrestrial habitats of the Nebraska Sandhills

Effects of drought-induced stress on nematode communities in aquatic and terrestrial habitats of the Nebraska Sandhills

Pond Water Microbiome Taxa Profiles and Antibiotic Resistance Genes Associated with Acidity and Tannins

Carbon and Nutrient Limitations of Microbial Metabolism in Xingkai Lake, China: Abiotic and Biotic Drivers

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