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16 pages, 2028 KiB

Open AccessArticle

Microbial Contamination in Urban Marine Sediments: Source Identification Using Microbial Community Analysis and Fecal Indicator Bacteria

by Ellinor M. Frank, Carolina Suarez, Isabel K. Erb, Therese Jephson, Elisabet Lindberg and Catherine J. Paul

Microorganisms 2025, 13(5), 983; https://doi.org/10.3390/microorganisms13050983 - 25 Apr 2025

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Abstract

We investigated the presence of the fecal indicator bacteria Escherichia coli, and other taxa associated with sewage communities in coastal sediments, near beaches with reported poor bathing water quality, focusing on the influence of effluent from a local wastewater treatment plant (WWTP) [...] Read more.

We investigated the presence of the fecal indicator bacteria Escherichia coli, and other taxa associated with sewage communities in coastal sediments, near beaches with reported poor bathing water quality, focusing on the influence of effluent from a local wastewater treatment plant (WWTP) and combined sewer overflows (CSO). Using a three-year dataset, we found that treated wastewater effluent is a significant source of sewage-associated taxa and viable E. coli in the sediments and that no seasonal differences were observed between spring and summer samples. CSO events have a local and temporary effect on the microbial community of sediments, distinct from that of treated wastewater effluent. Sediments affected by CSO had higher abundances of families Lachnospiraceae, Ruminococcaceae, and Bacteroidaceae. Sewage releases may also impact the natural community of the sediments, as higher abundances of marine sulfur-cycling bacteria were noticed in locations where sewage taxa were also abundant. Microbial contamination at locations distant from known CSO and treatment plant outlets suggests additional sources, such as stormwater. This study highlights that while coastal sediments can be a reservoir of E. coli and contain sewage-associated taxa, their distribution and potential origins are complex and are likely not linked to a single source. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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16 pages, 6507 KiB

Open AccessArticle

The Effects of Varying Concentrations of Didecyl Methylpropyl Ammonium Iodide (DMPAI) on the Structure and Function of Soil Bacterial Communities in the Lake–Terrestrial Ecotone

by Qi Zhu, Lingquan Zeng, Chunhua Li and Chun Ye

Microorganisms 2025, 13(4), 934; https://doi.org/10.3390/microorganisms13040934 - 18 Apr 2025

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Abstract

To address freshwater lake blooms resulting from eutrophication, the application of quaternary ammonium compounds as algaecides serves as an effective emergency remediation strategy. Didecyl methylpropyl ammonium iodide (DMPAI) is a novel quaternary ammonium algaecide; however, its bacteriostatic properties may significantly disrupt the microbial [...] Read more.

To address freshwater lake blooms resulting from eutrophication, the application of quaternary ammonium compounds as algaecides serves as an effective emergency remediation strategy. Didecyl methylpropyl ammonium iodide (DMPAI) is a novel quaternary ammonium algaecide; however, its bacteriostatic properties may significantly disrupt the microbial activity in lakes, particularly within the lake–terrestrial ecotone. To investigate the degradation process of DMPAI in the lake–terrestrial ecotone and its impact on the microbial community, experiments were conducted using a large-scale indoor simulation device to analyze DMPAI concentrations, the composition of the lake microbial community, and associated gene functions. The results showed that (1) DMPAI was completely removed from the lake water body in approximately 36 h; (2) The addition of DMPAI altered the microbial community structure in the lake–terrestrial ecotone, as evidenced by an increase in the diversity index and the proliferation of microorganisms capable of tolerating and degrading DMPAI, such as Pseudomonas and Flavobacterium, within a short period. These changes were typically observed after 10 d and generally recovered, not persisting for extended periods. (3) Functional genes involved in carbon, nitrogen, and sulfur cycling are more significantly impaired in the lake–terrestrial ecotone with DMPAI addition. The destabilization of the microbial community may lead to a short-term increase in pathogenic bacteria during the recovery process. This phenomenon was more pronounced in environments with higher concentrations of DMPAI. Therefore, the concentration of DMPAI should be controlled within the range of 0.5 to 2.0 mg L⁻¹. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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16 pages, 3880 KiB

Open AccessArticle

Microbial Communities in and Around the Siboglinid Tubeworms from the South Yungan East Ridge Cold Seep Offshore Southwestern Taiwan at the Northern South China Sea

by Yin Li, Zhiwei Ye, Mei-Chin Lai, Char-Shine Liu, Charles K. Paull, Saulwood Lin, Shu-Jung Lai, Yi-Ting You, Sue-Yao Wu, Chuan-Chuan Hung, Jiun-Yan Ding, Chao-Jen Shih, Yen-Chi Wu, Jingjing Zhao, Wangchuan Xiao, Chih-Hung Wu, Guowen Dong, Hangying Zhang, Wanling Qiu, Song Wang and Sheng-Chung Chen Show full author list Hide full author list

Microorganisms 2024, 12(12), 2452; https://doi.org/10.3390/microorganisms12122452 - 28 Nov 2024

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Abstract

To date, only a few microbial community studies of cold seeps at the South China Sea (SCS) have been reported. The cold seep dominated by tubeworms was discovered at South Yungan East Ridge (SYER) offshore southwestern Taiwan by miniROV. The tubeworms were identified [...] Read more.

To date, only a few microbial community studies of cold seeps at the South China Sea (SCS) have been reported. The cold seep dominated by tubeworms was discovered at South Yungan East Ridge (SYER) offshore southwestern Taiwan by miniROV. The tubeworms were identified and proposed as Paraescarpia formosa sp. nov. through morphological and phylogenetic analyses. The endosymbionts in the trunk of P. formosa analyzed by a 16S rRNA gene clone library represented only one phylotype, which belonged to the family Sedimenticolaceae in Gammaproteobacteria. In addition, the archaeal and bacterial communities in the habitat of tubeworm P. formosa were investigated by using high-phylogenetic-resolution full-length 16S rRNA gene amplicon sequencing. The results showed that anerobic methane-oxidizing archaea (ANME)-1b was most abundant and ANME-2ab was minor in a consortia of the anerobic oxidation of methane (AOM). The known sulfate-reducing bacteria (SRB) partners in AOM consortia, such as SEEP-SRB1, -SRB2, and -SRB4, Desulfococcus and Desulfobulbus, occurred in a small population (0–5.7%) at the SYER cold seep, and it was suggested that ANME-1b and ANME-2ab might be coupled with multiple SRB in AOM consortia. Besides AOM consortia, various methanogenic archaea, including Bathyarchaeota (Subgroup-8), Methanocellales, Methanomicrobiales, Methanosarcinales, Methanofastidiosales and Methanomassiliicoccales, were identified, and sulfur-oxidizing bacteria Sulfurovum and Sulfurimonas in phylum Epsilonbacteraeota were dominant. This study revealed the first investigation of microbiota in and around tubeworm P. formosa discovered at the SYER cold seep offshore southwestern Taiwan. We could gain insights into the chemosynthetic communities in the deep sea, especially regarding the cold seep ecosystems at the SCS. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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18 pages, 3561 KiB

Open AccessArticle

The Effects of Low Concentrations and Long-Term Contamination by Sodium Dodecyl Sulfate on the Structure and Function of Bacterial Communities in the Lake–Terrestrial Ecotone

by Lingquan Zeng, Qi Zhu, Chunhua Li and Chun Ye

Microorganisms 2024, 12(11), 2330; https://doi.org/10.3390/microorganisms12112330 - 15 Nov 2024

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Abstract

Due to the growing focus on daily hygiene practices, sodium dodecyl sulfate (SDS), a widely used surfactant, is increasingly found in domestic sewage and rainfall runoff. Upon entering the lake–terrestrial ecotone, SDS affects the composition, abundance, and functional capacity of soil bacterial communities [...] Read more.

Due to the growing focus on daily hygiene practices, sodium dodecyl sulfate (SDS), a widely used surfactant, is increasingly found in domestic sewage and rainfall runoff. Upon entering the lake–terrestrial ecotone, SDS affects the composition, abundance, and functional capacity of soil bacterial communities due to its bacteriostatic properties. To investigate the effects of long-term discharge of sewage containing low concentrations of SDS on microorganisms in the lake–terrestrial ecotone, alterations in bacterial community structure, functional genes, and biomass were examined using a simulated continuous pollutant input. The results indicated the following: (1) The degradation rate of sodium dodecyl sulfate (SDS) by soil microorganisms in the lake–terrestrial ecotone under long-term and low concentrations of SDS stress ranged from 11 to 16 mg/kg·d. (2) The effects of low concentrations and long-term SDS stress on bacterial community structure and gene function in the lake–terrestrial ecotone differed significantly from those of short-term pollution. The damage to microbial-promoted material cycling in the lake–terrestrial ecotone was more severe; however, the proliferation of pathogenic bacteria remained continuously suppressed. (3) Soil bacteria in the lake–terrestrial ecotone responded to the stress of long-term and low concentrations of SDS primarily by enhancing chemotaxis and tolerance. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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17 pages, 1593 KiB

Open AccessArticle

Impact of Top-Down Regulation on the Growth Efficiency of Freshwater Bacterioplankton

by Angia Sriram Pradeep Ram, Hermine Billard, Fanny Perriere, Olivier Voldoire and Jonathan Colombet

Microorganisms 2024, 12(10), 2061; https://doi.org/10.3390/microorganisms12102061 - 15 Oct 2024

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Abstract

To investigate the hypothesis of top-down control by viruses and heterotrophic nanoflagellates on bacterial-mediated carbon fluxes in freshwater systems, a year-long study (2023–2024) was conducted in the pelagic zone of Lake Saint-Gervais (France). The variability in BGE (9.9% to 45.5%) was attributed to [...] Read more.

To investigate the hypothesis of top-down control by viruses and heterotrophic nanoflagellates on bacterial-mediated carbon fluxes in freshwater systems, a year-long study (2023–2024) was conducted in the pelagic zone of Lake Saint-Gervais (France). The variability in BGE (9.9% to 45.5%) was attributed to the decoupling of production and respiration, providing bacterioplankton communities with a competitive advantage in adapting to fluctuating environmental disturbances in freshwater systems. The high nucleic acid (HNA) bacterial community, the active fraction, contributed the most to bacterial production and was linked to BGE estimates. Weak bottom-up controls (nutrient concentrations and stoichiometry) on BGE suggested a stronger role for mortality forces. Among viral subgroups (VLP1–VLP4) identified via flow cytometry, the dominant low-fluorescence DNA VLP1 subgroup (range = 0.7 to 3.1 × 10⁸ VLP mL⁻¹) accounting for the majority of viral production was closely linked to the HNA population. Both top-down forces exerted antagonistic effects on BGE at the community level. The preferential lysis and grazing of the susceptible HNA population, which stimulated bacterial community respiration more than production in the non-target population, resulted in reduced BGE. These results underscore the key role of top-down processes in shaping carbon flux through bacterioplankton in this freshwater system. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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15 pages, 12286 KiB

Open AccessArticle

Spatial and Seasonal Changes in Microbial Community of Hynobius amjiensis Breeding Pools in a Sphagnum-Dominated Peatland

by Meng-Jie Yu, Xian-Ting Wang, Ting Wang, Wei-Quan Huang, Ze-Dong Lang, Jia-Peng Wang and Yu-Huan Wu

Microorganisms 2024, 12(7), 1344; https://doi.org/10.3390/microorganisms12071344 - 30 Jun 2024

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Abstract

Peatlands deliver a variety of beneficial ecosystem services, particularly serving as habitats for a diverse array of species. Hynobius amjiensis is a critically endangered amphibian initially discovered in a Sphagnum-dominated peatland in Anji, China. The unique habitat requirements of H. amjiensis make [...] Read more.

Peatlands deliver a variety of beneficial ecosystem services, particularly serving as habitats for a diverse array of species. Hynobius amjiensis is a critically endangered amphibian initially discovered in a Sphagnum-dominated peatland in Anji, China. The unique habitat requirements of H. amjiensis make it highly vulnerable to environmental changes. Here, we investigated the different breeding pools of H. amjiensis in the Sphagnum-dominated peatland (the type locality) for a one-year period to evaluate the interactions among the egg sacs present, water quality, and microbial communities (16S and 18S rRNA gene amplicon). The numbers of egg sacs were higher in the breeding pools located at the marginal area than those at the core area of the peatland. Similarly, the α-diversity of bacteria, fungi, and protists were lower in the core region compared to those at the edge of the peatland, perhaps due to water eutrophication. The microbial communities and water quality differed significantly among breeding pools and sampling months. The simpler microbial networks of the breeding pools in the core wetland may impact the numbers and health of the egg sacs. This study contributes to a better understanding of the effect of water quality on biodiversity in peatlands, and it can also guide regulations for wetland conservation and the protection of endangered species. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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17 pages, 10721 KiB

Open AccessArticle

Bacterial Diversity and Vertical Distribution Patterns in Sandy Sediments: A Study on the Bacterial Community Structure Based on Environmental Factors in Tributaries of the Yangtze River

by Tian Zhang, Weibo Wang, Yifei Leng, Yu Huang, Wen Xiong and Fengyi Chang

Microorganisms 2024, 12(6), 1178; https://doi.org/10.3390/microorganisms12061178 - 11 Jun 2024

Cited by 1 | Viewed by 1340

Abstract

Bacterial diversity and its distribution characteristics in sediments are critical to understanding and revealing biogeochemical cycles in sediments. However, little is known about the relationship between biogeochemistry processes and vertical spatial distribution of bacterial communities in sandy sediments. In this study, we used [...] Read more.

Bacterial diversity and its distribution characteristics in sediments are critical to understanding and revealing biogeochemical cycles in sediments. However, little is known about the relationship between biogeochemistry processes and vertical spatial distribution of bacterial communities in sandy sediments. In this study, we used fluorescence quantitative PCR, high-throughput sequencing technology and statistical analysis to explore the vertical distribution pattern of bacterial community diversity and its influencing factors in sandy sediments of the Yangtze River Basin. The aim is to enrich the understanding of the ecological characteristics and functions of bacteria in river ecosystems. The results showed that both sediment bacterial abundance and diversity showed a gradual decrease from surface to bottom in the vertical distribution. The main environmental factors that influenced the bacterial distribution pattern were pore water dissolved oxygen (DO), total nitrogen (TN) concentration and sediment nitrogen (N) content. The dominant bacterial species, Massilia and Flavobacterium, are suitable for growth and reproduction in high oxygen and nutrient-richer environments, while Limnobacter prefers low oxygen or anaerobic conditions. The vertical distribution pattern of bacteria and its influencing factors in river sandy sediment found in this study differ from the results in mud sediment, which may be related to the larger granular gap between sandy sediment and the lower content of organic matter. The findings of this study further our understanding of the distribution patterns and ecological preferences of microbial communities in river sediments, providing insights into how these communities may adapt to varying environmental conditions. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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17 pages, 8725 KiB

Open AccessArticle

The Vertical Metabolic Activity and Community Structure of Prokaryotes along Different Water Depths in the Kermadec and Diamantina Trenches

by Hao Liu and Hongmei Jing

Microorganisms 2024, 12(4), 708; https://doi.org/10.3390/microorganisms12040708 - 30 Mar 2024

Cited by 1 | Viewed by 1678

Abstract

Prokaryotes play a key role in particulate organic matter’s decomposition and remineralization processes in the vertical scale of seawater, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity of the [...] Read more.

Prokaryotes play a key role in particulate organic matter’s decomposition and remineralization processes in the vertical scale of seawater, and prokaryotes contribute to more than 70% of the estimated remineralization. However, little is known about the microbial community and metabolic activity of the vertical distribution in the trenches. The composition and distribution of prokaryotes in the water columns and benthic boundary layers of the Kermadec Trench and the Diamantina Trench were investigated using high-throughput sequencing and quantitative PCR, together with the Biolog Ecoplate^TM microplates culture to analyze the microbial metabolic activity. Microbial communities in both trenches were dominated by Nitrososphaera and Halobacteria in archaea, and by Alphaproteobacteria and Gammaproteobacteria in bacteria, and the microbial community structure was significantly different between the water column and the benthic boundary layer. At the surface water, amino acids and polymers were used preferentially; at the benthic boundary layers, amino acids and amines were used preferentially. Cooperative relationships among different microbial groups and their carbon utilization capabilities could help to make better use of various carbon sources along the water depths, reflected by the predominantly positive relationships based on the co-occurrence network analysis. In addition, the distinct microbial metabolic activity detected at 800 m, which was the lower boundary of the twilight zone, had the lowest salinity and might have had higher proportions of refractory carbon sources than the shallower water depths and benthic boundary layers. This study reflected the initial preference of the carbon source by the natural microbes in the vertical scale of different trenches and should be complemented with stable isotopic tracing experiments in future studies to enhance the understanding of the complex carbon utilization pathways along the vertical scale by prokaryotes among different trenches. Full article

(This article belongs to the Special Issue Microbial Communities in Aquatic Environments)

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