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Vaughn SN, Atkinson CL, Johnson PD, Jackson CR. Characterizing the Gut Microbial Communities of Native and Invasive Freshwater Bivalves after Long-Term Sample Preservation. Microorganisms 2023; 11:2489. [PMID: 37894147 PMCID: PMC10609060 DOI: 10.3390/microorganisms11102489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 10/02/2023] [Accepted: 10/02/2023] [Indexed: 10/29/2023] Open
Abstract
Freshwater mussels are important indicators of the overall health of their environment but have suffered declines that have been attributed to factors such as habitat degradation, a loss of fish hosts, climate change, and excessive nutrient inputs. The loss of mussel biodiversity can negatively impact freshwater ecosystems such that understanding the mussel's gut microbiome has been identified as a priority topic for developing conservation strategies. In this study, we determine whether ethanol-stored specimens of freshwater mussels can yield representative information about their gut microbiomes such that changes in the microbiome through time could potentially be determined from museum mussel collections. A short-term preservation experiment using the invasive clam Corbicula fluminea was used to validate the use of ethanol as a method for storing the bivalve microbiome, and the gut microbiomes of nine native mussel species that had been preserved in ethanol for between 2 and 9 years were assessed. We show that ethanol preservation is a valid storage method for bivalve specimens in terms of maintaining an effective sequencing depth and the richness of their gut bacterial assemblages and provide further insight into the gut microbiomes of the invasive clam C. fluminea and nine species of native mussels. From this, we identify a "core" genus of bacteria (Romboutsia) that is potentially common to all freshwater bivalve species studied. These findings support the potential use of ethanol-preserved museum specimens to examine patterns in the gut microbiomes of freshwater mussels over long periods.
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Affiliation(s)
- Stephanie N. Vaughn
- Department of Biology, University of Mississippi, University, MS 38677, USA;
| | - Carla L. Atkinson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, AL 35487, USA;
| | - Paul D. Johnson
- Alabama Department of Conservation and Natural Resources, Alabama Aquatic Biodiversity Center, Marion, AL 36756, USA;
| | - Colin R. Jackson
- Department of Biology, University of Mississippi, University, MS 38677, USA;
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Gao J, Zhi Y, Huang Y, Shi S, Tan Q, Wang C, Han L, Yao J. Effects of benthic bioturbation on anammox in nitrogen removal at the sediment-water interface in eutrophic surface waters. WATER RESEARCH 2023; 243:120287. [PMID: 37451126 DOI: 10.1016/j.watres.2023.120287] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/18/2023]
Abstract
Anaerobic ammonium oxidation (anammox) significantly contributes to nitrogen loss in freshwater ecosystems. The sediment-water interface (SWI), known as a "hot spot" for anammox, also harbors numerous macroinvertebrates. However, the impact of their bioturbation on anammox has generally been overlooked. This study compared the effects of three representative macroinvertebrates (i.e., Propsilocerus akamusi, Branchiura sowerbyi and Radix swinhoei) with different bioturbation modes on anammox and the N-removal processes at the SWI by using a microcosmic system. The results demonstrated that all three benthic macroinvertebrates promoted anammox in addition to denitrification processes. The highest N-removal was achieved in the presence of P. akamusi considered as a gallery-diffuser, where the relative abundance of Planctomycetes (to which the anammox bacteria belong) increased by 70%. P. akamusi increased the abundance of anammox hzsB gene by 2.58-fold and promoted potential anammox rate by 12.79 nmol N g-1 h-1, which in turn facilitated total N-removal mass increased by 2.42-fold. In the presence of B. sowerbyi and R. swinhoei, the potential anammox rates increased by 4.81 and 5.57 nmol N g-1 h-1, respectively. These results underscore the substantial impact of macroinvertebrates on anammox and N-removal processes, highlighting their crucial role in N pollution control, and sustaining the overall health and stability of eutrophic water bodies.
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Affiliation(s)
- Jie Gao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yue Zhi
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Yuyue Huang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Sijie Shi
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Qiujun Tan
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Chengcheng Wang
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Le Han
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China
| | - Jingmei Yao
- Key Laboratory of Eco-Environments in Three Gorges Reservoir Region, Ministry of Education, Chongqing University, Chongqing 400045, China; College of Environment and Ecology, Chongqing University, Chongqing 400045, China.
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Millar EN, Kidd KA, Surette MG, Bennett CJ, Salerno J, Gillis PL. Effects of municipal wastewater effluents on the digestive gland microbiome of wild freshwater mussels (Lasmigona costata). ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 241:113774. [PMID: 35777341 DOI: 10.1016/j.ecoenv.2022.113774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 06/07/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
Gut microbial communities are vital for maintaining host health, and are sensitive to diet, environment, and chemical exposures. Wastewater treatment plants (WWTPs) release effluents containing antimicrobials, pharmaceuticals, and other contaminants that may negatively affect the gut microbiome of downstream organisms. This study investigated changes in the diversity and composition of the digestive gland microbiome of flutedshell mussels (Lasmigona costata) from upstream and downstream of two large (service >100,000) WWTPs. Mussel digestive gland microbiome was analyzed following the extraction, PCR amplification, and sequencing of bacterial DNA using the V3-V4 hypervariable regions of the 16 S rRNA gene. Bacterial alpha diversity decreased at sites downstream of the second WWTP and these sites were dissimilar in beta diversity from sites upstream and downstream of the first upstream WWTP. The microbiomes of mussels collected downstream of the first WWTP had increased relative abundances of Actinobacteria, Bacteroidetes, and Firmicutes, with a decrease in Cyanobacteria, compared to upstream mussels. Meanwhile, those collected downstream of the second WWTP increased in Proteobacteria and decreased in Actinobacteria, Bacteroidetes, and Tenericutes. Increased Proteobacteria has been linked to adverse effects in mammals, but their functions in mussels is currently unknown. Finally, effluent-derived bacteria were found in the microbiome of mussels downstream of both WWTPs but not in those from upstream. Overall, results show that the digestive gland microbiome of mussels collected upstream and downstream of WWTPs differed, which has implications for altered host health and the transport of WWTP-derived bacteria through aquatic ecosystems.
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Affiliation(s)
- Elise N Millar
- Department of Biology, McMaster University, Hamilton, Ontario, Canada
| | - Karen A Kidd
- Department of Biology, McMaster University, Hamilton, Ontario, Canada; School of Earth, Environment and Society, McMaster University, Hamilton, Ontario, Canada.
| | - Michael G Surette
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada; Department of Medicine, McMaster University, Hamilton, Ontario, Canada
| | - C James Bennett
- Aquatic Contaminants Research Division, Water Science and Technology Directorate, Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Joseph Salerno
- Aquatic Contaminants Research Division, Water Science and Technology Directorate, Environment and Climate Change Canada, Burlington, Ontario, Canada
| | - Patricia L Gillis
- Aquatic Contaminants Research Division, Water Science and Technology Directorate, Environment and Climate Change Canada, Burlington, Ontario, Canada
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Morales J. Assessment of endangered freshwater pearl mussel populations in the Northern Iberian Plateau in relation to non–native species: xenodiversity as a threat. ANIMAL BIODIVERSITY AND CONSERVATION 2022. [DOI: 10.32800/abc.2022.45.0203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In the last two decades, small populations of freshwater pearl mussels, Margaritifera margaritifera, have been recorded in Mediterranean rivers of the Iberian Northern Plateau. A survey was carried out in Castilla and León in 2018 to assess the development of populations of this species in all the rivers of known distribution and to update the threat classification. Thirty sections in the rivers Negro, Tera, Alberche and Águeda were positive for its presence, and another 50 stretches of seven rivers were negative. The species is currently distributed over about 22.5 km. Águeda and Tera populations have decreased dramatically in the last 14 years and are on the threshold of extinction. The Negro river supports the largest population, although the species has now disappeared in at least 61 % of the stretches that were inhabited in 2004. All populations showed very low densities and an ageing population structure, with no recruitment for decades. The presence of non-native invasive alien species (NIS) was higher than in a previous regional survey, with the signal crayfish representing the greatest threat. We observed changes in benthic microhabitats and direct predation of adults and glochidia conglutinates. In the Alberche River, in strict syntopy with M. margaritifera and two other mussel species, 10 NIS were detected. The current hydrological and ecological conditions in the Duero watershed support the settlement of exotic species to the disadvantage of native mollusks, which are more demanding in terms of microhabitats.
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Biofilm Bacterial Dynamics and Changes in Inorganic Nitrogen Density Due to the Presence of Freshwater Pearl Mussels. mSphere 2022; 7:e0083421. [PMID: 35138127 PMCID: PMC8826952 DOI: 10.1128/msphere.00834-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The freshwater pearl mussel (genus Margaritifera) has shown severe declines, while the mussels play important roles in the translocation of nutrients and materials in river water ecosystems. We hypothesized that the biofilm bacterial composition and nutrient flow may reflect the differences in the existence of mussels. We analyzed water from 14 rivers from in multiple regions of Japan, including eight rivers, where the two species of freshwater pearl mussels (Margaritifera laevis and Margaritifera togakushiensis) are predominantly found, to analyze the microbial and nutritional nature of the biofilm artificially formed in the river. Field-produced biofilms, including the bacterial community structure, were examined, using next-generation sequencing of bacterial 16S rRNA gene amplicons followed by analyzing the genomic DNA extracted from the samples, inorganic nitrogen compounds, and chlorophyll a concentration. Compared to those in the control river without freshwater pearl mussels, biofilms of the existing river contained less inorganic nitrogen (ammonia and nitrate), suggesting the involvement of mussels in regulating the river water nutrient flow. Distinct changes were found in biofilms, depending on mussel existence, particularly in biofilms containing fewer photosynthetic bacterial groups, such as Betaproteobacteria and Cyanobacteria. Conversely, bacteria belonging to Bacteroidales in Bacteroidetes and Clostridiales in Firmicutes were predominantly found in biofilm samples where the mussels existed. Mussels alleviated strict nitrogen limitation in streams and possibly caused a concomitant change in the bacterial communities, where populations of bacterial groups exchanging inorganic nitrogen were low. We demonstrate the profound influence of freshwater mussel species on ecosystem processes and community dynamics across rivers. IMPORTANCE The abundance of freshwater unioid mussels exhibited more diverse patterns of inorganic nitrogen flow and bacterial communities than the areas without mussels. This study demonstrates the effect of mussels on different freshwater ecosystem processes with variable organismal densities and biogeochemical factors. Freshwater unionid mussels significantly affect the ecosystem and community dynamics by modulating the relationships, altering nutrient availability, and indirectly manipulating the downstream ecological members, eventually expanding their role in the river ecosystems.
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Higgins E, Parr TB, Vaughn CC. Mussels and Local Conditions Interact to Influence Microbial Communities in Mussel Beds. Front Microbiol 2022; 12:790554. [PMID: 35095802 PMCID: PMC8793333 DOI: 10.3389/fmicb.2021.790554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Microbiomes are increasingly recognized as widespread regulators of function from individual organism to ecosystem scales. However, the manner in which animals influence the structure and function of environmental microbiomes has received considerably less attention. Using a comparative field study, we investigated the relationship between freshwater mussel microbiomes and environmental microbiomes. We used two focal species of unionid mussels, Amblema plicata and Actinonaias ligamentina, with distinct behavioral and physiological characteristics. Mussel microbiomes, those of the shell and biodeposits, were less diverse than both surface and subsurface sediment microbiomes. Mussel abundance was a significant predictor of sediment microbial community composition, but mussel species richness was not. Our data suggest that local habitat conditions which change dynamically along streams, such as discharge, water turnover, and canopy cover, work in tandem to influence environmental microbial community assemblages at discreet rather than landscape scales. Further, mussel burrowing activity and mussel shells may provide habitat for microbial communities critical to nutrient cycling in these systems.
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Affiliation(s)
- Edward Higgins
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
- *Correspondence: Edward Higgins,
| | - Thomas B. Parr
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
- National Park Service, Great Lakes Inventory and Monitoring Network, Ashland, WI, United States
| | - Caryn C. Vaughn
- Oklahoma Biological Survey and Department of Biology, University of Oklahoma, Norman, OK, United States
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7
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Zhang Y, Meng C, He Y, Wang X, Xue G. Influence of cell lysis by Fenton oxidation on cryptic growth in sequencing batch reactor (SBR): Implication of reducing sludge source discharge. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 789:148042. [PMID: 34323827 DOI: 10.1016/j.scitotenv.2021.148042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/21/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
The cell lysis-cryptic growth was implemented by Fenton oxidation in sequencing batch reactor. Optimizing sludge lysis condition could maximize the release of nutrients and sludge disintegration degree. After Fenton oxidation, the extracellular polymeric substance was obviously destroyed with the sludge average particle decreased from 64 μm to 36 μm. After 5% of the settled sludge in sequencing batch reactor (SBR) was oxidized by Fenton and then returned to SBR, the mixed liquor suspended solids (MLSS) decreased by 19.3% at the end of 35 days operation, the average mixed liquor volatile suspended solids/mixed liquor suspended solids (MLVSS/MLSS) was promoted by 13.3% during the entire operation. Returning lysed sludge had no significant influence on the organics and nitrogen removal, but the total phosphorus removal was distinctly enhanced by generating FePO4 precipitate. Additionally, returning lysed sludge suppressed nitrifying bacteria and promoted denitrifying bacteria slightly. Consequently, the cell lysis-cryptic growth for reducing sludge source discharge from wastewater biological treatment could be achieved on the premise of ensuring effluent quality.
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Affiliation(s)
- Yu Zhang
- School of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Chengcheng Meng
- School of Environmental Science and Engineering, Donghua University, Shanghai 201620, China; Tianjin United Environmental Protection Engineering Design Co., Ltd., Tianjin 300110, China
| | - Yueling He
- School of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Xiaonuan Wang
- School of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Gang Xue
- School of Environmental Science and Engineering, Donghua University, Shanghai 201620, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200000, China; National Engineering Research Center for Dyeing and Finishing of Textiles, Shanghai 201620, China.
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8
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Li H, Yang XR, Wang J, Zhou GW, Zhang YS, Lassen SB, Zhu YG, Su JQ. Earthworm gut: An overlooked niche for anaerobic ammonium oxidation in agricultural soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 752:141874. [PMID: 32889284 DOI: 10.1016/j.scitotenv.2020.141874] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/18/2020] [Accepted: 08/19/2020] [Indexed: 06/11/2023]
Abstract
Soil fauna takes an active part in accelerating turnover of nutrients in terrestrial ecosystems. Anaerobic ammonium oxidation (anammox) has been widely characterized, however, whether anammox is active in earthworm gut and the effect of earthworm on anammox in soil remain unknown. In this study, the activity, abundance and community of anammox bacteria in earthworm guts and soils from microcosms were determined using a 15N-tracing technique, quantitative PCR, and anammox bacterial 16S rRNA gene amplicon sequencing. Results showed that anammox rates in guts ranged between 5.81 and 14.19 nmol N g-1 dw gut content h-1, which were significantly (P < 0.01) higher than that in their surrounding soils during 30 day incubation. On the contrary, abundances of hzsB genes encoding subunit B hydrazine synthase in guts were significantly (P < 0.05) lower than those in their surrounding soils. Anammox rates, denitrification N2 production rates and hzsB genes in soils with earthworms were significantly (P < 0.05) lower than those in control soils. Anammox bacterial compositions differed significantly (P < 0.05) between gut and soil, and earthworm altered anammox bacterial communities in soils. Brocadia, Kuenenia and abundant unclassified anammox bacteria were detected in collected soils and gut contents, in which Brocadia was only detected in guts. These results suggested that microbes in earthworm gut increase, but present of earthworm reduces anammox and denitrification associated N loss by altering the anammox bacterial community compositions in soils.
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Affiliation(s)
- Hu Li
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xiao-Ru Yang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Juan Wang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Ningbo Key Lab of Urban Environment Process and Pollution Control, Ningbo Urban Environment Observation and Research Station-NUEORS, Chinese Academy of Sciences, No. 88 Zhong Ke Road, Ningbo 315830, China
| | - Guo-Wei Zhou
- State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yu-Sen Zhang
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Simon Bo Lassen
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg, Denmark
| | - Yong-Guan Zhu
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; State Key Laboratory of Urban and Regional Ecology Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Jian-Qiang Su
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China.
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Weingarten EA, Atkinson CL, Jackson CR. The gut microbiome of freshwater Unionidae mussels is determined by host species and is selectively retained from filtered seston. PLoS One 2019; 14:e0224796. [PMID: 31721801 PMCID: PMC6853330 DOI: 10.1371/journal.pone.0224796] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/22/2019] [Indexed: 01/06/2023] Open
Abstract
Freshwater mussels are a species-rich group of aquatic invertebrates that are among the most endangered groups of fauna worldwide. As filter-feeders that are constantly exposed to new microbial inoculants, mussels represent an ideal system to investigate the effects of species or the environment on gut microbiome composition. In this study, we examined if host species or site exerts a greater influence on microbiome composition. Individuals of four co-occurring freshwater mussel species, Cyclonaias asperata, Fusconaia cerina, Lampsilis ornata, and Obovaria unicolor were collected from six sites along a 50 km stretch of the Sipsey River in Alabama, USA. High throughput 16S rRNA gene sequencing revealed that mussel gut bacterial microbiota were distinct from bacteria on seston suspended in the water column, and that the composition of the gut microbiota was influenced by both host species and site. Despite species and environmental variation, the most frequently detected sequences within the mussel microbiota were identified as members of the Clostridiales. Sequences identified as the nitrogen-fixing taxon Methylocystis sp. were also abundant in all mussel species, and sequences of both bacterial taxa were more abundant in mussels than in water. Site physicochemical conditions explained almost 45% of variation in seston bacterial communities but less than 8% of variation in the mussel bacterial microbiome. Together, these findings suggest selective retention of bacterial taxa by the freshwater mussel host, and that both species and the environment are important in determining mussel gut microbiome composition.
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Affiliation(s)
- Eric A. Weingarten
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
| | - Carla L. Atkinson
- Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, United States of America
| | - Colin R. Jackson
- Department of Biology, University of Mississippi, University, Mississippi, United States of America
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10
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Shi R, Xu S, Qi Z, Zhu Q, Huang H, Weber F. Influence of suspended mariculture on vertical distribution profiles of bacteria in sediment from Daya Bay, Southern China. MARINE POLLUTION BULLETIN 2019; 146:816-826. [PMID: 31426223 DOI: 10.1016/j.marpolbul.2019.07.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/18/2019] [Accepted: 07/18/2019] [Indexed: 06/10/2023]
Abstract
Mariculture is known to contribute to oxygen depletion, pH decline and accumulation of nutrients and organic matter in sediments. However, studies on the bacterial vertical distribution of mariculture area are very limited. The bacterial abundance in the non-culture site (3.8 ± 0.8 × 109 copies g-1) was significantly higher than that in the three mariculture sites (1.2 ± 0.2 × 109 copies g-1), and bacterial diversity in the non-culture site was significantly higher than that in fish cage-TF (p < 0.05). The vertical distribution profiles of bacteria in non-culture and oyster culture sites were similar but very different from that of fish cage-TF. In addition, significant downward trends in bacterial abundance and diversity were observed as sediment depth increased (p < 0.05), and the most relevant environmental factors were moisture content, total nitrogen, total organic carbon and carbon/nitrogen. The dominant bacterial phyla in sediment were Proteobacteria, Chloroflexi and Bacteroidetes.
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Affiliation(s)
- Rongjun Shi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Shumin Xu
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Zhanhui Qi
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China.
| | - Qingzhi Zhu
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA.
| | - Honghui Huang
- Guangdong Provincial Key Laboratory of Fishery Ecology and Environment and Key Laboratory of Open-Sea Fishery Development, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Science, Guangzhou 510300, PR China
| | - Felix Weber
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY 11794-5000, USA
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11
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Murphy AE, Kolkmeyer R, Song B, Anderson IC, Bowen J. Bioreactivity and Microbiome of Biodeposits from Filter-Feeding Bivalves. MICROBIAL ECOLOGY 2019; 77:343-357. [PMID: 30612185 DOI: 10.1007/s00248-018-01312-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 12/20/2018] [Indexed: 06/09/2023]
Abstract
Bivalves serve an important ecosystem function in delivering organic matter from pelagic to benthic zones and are important in mediating eutrophication. However, the fate of this organic matter (i.e., biodeposits) is an important consideration when assessing the ecological roles of these organisms in coastal ecosystems. In addition to environmental conditions, the processing of biodeposits is dependent on its composition and the metabolic capacity of the associated microbial community. The objectives of this study were to compare the biological reactivity, potential denitrification rates, and microbial communities of biodeposits sourced from different bivalve species: hard clam (Mercenaria mercenaria), eastern oyster (Crassostrea virginica), and ribbed mussel (Geukensia demissa). To our knowledge, this is the first study to investigate and compare the microbiome of bivalve biodeposits using high-throughput sequencing and provide important insight into the mechanisms by which bivalves may alter sediment microbial communities and benthic biogeochemical cycles. We show that clam biodeposits had significantly higher bioreactivity compared to mussel and oyster biodeposits, as reflected in higher dissolved inorganic carbon and ammonium production rates in controlled incubations. Potential denitrification rates were also significantly higher for clam biodeposits compared to oyster and mussel biodeposits. The microbial communities associated with the biodeposits were significantly different across bivalve species, with significantly greater abundances of Alteromonadales, Chitinophagales, Rhodobacterales, and Thiotrichales associated with the clam biodeposits. These bioreactivity and microbial differences across bivalve species are likely due to differences in bivalve physiology and feeding behavior and should be considered when evaluating the effects of bivalves on water quality and ecosystem function.
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Affiliation(s)
- Anna E Murphy
- Marine Science Center, Northeastern University, Nahant, MA, 01908, USA.
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA.
| | | | - Bongkuen Song
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Iris C Anderson
- College of William & Mary, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Jennifer Bowen
- Marine Science Center, Northeastern University, Nahant, MA, 01908, USA
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12
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Zhang B, Xu X, Zhu L. Activated sludge bacterial communities of typical wastewater treatment plants: distinct genera identification and metabolic potential differential analysis. AMB Express 2018; 8:184. [PMID: 30430271 PMCID: PMC6236004 DOI: 10.1186/s13568-018-0714-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 11/07/2018] [Indexed: 12/26/2022] Open
Abstract
To investigate the differences in activated sludge microbial communities of different wastewater treatment plants (WWTPs) and understand their metabolic potentials, we sampled sludge from every biological treatment unit of 5 full-scale waste water treatment systems in 3 typical Chinese municipal WWTPs. The microbial communities and overall metabolic patterns were not only affected by influent characteristics but also varied between different biological treatment units. Distinct genera in different wastewater treatment systems were identified. The important microorganisms in domestic sewage treatment systems were unclassified SHA-20, Caldilinea, Dechloromonas, and unclassified genera from Rhodospirilaceae and Caldilineaceae. The important microorganisms in dyeing wastewater treatment systems were Nitrospira, Sphingobacteriales, Thiobacillus, Sinobacteraceae and Comamonadaceae. Compared with the obvious differences in microbial community composition, the metabolic potential showed no significant differences.
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13
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Md Zoqratt MZH, Eng WWH, Thai BT, Austin CM, Gan HM. Microbiome analysis of Pacific white shrimp gut and rearing water from Malaysia and Vietnam: implications for aquaculture research and management. PeerJ 2018; 6:e5826. [PMID: 30397546 PMCID: PMC6214229 DOI: 10.7717/peerj.5826] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/25/2018] [Indexed: 01/27/2023] Open
Abstract
Aquaculture production of the Pacific white shrimp is the largest in the world for crustacean species. Crucial to the sustainable global production of this important seafood species is a fundamental understanding of the shrimp gut microbiota and its relationship to the microbial ecology of shrimp pond. This is especially true, given the recently recognized role of beneficial microbes in promoting shrimp nutrient intake and in conferring resistance against pathogens. Unfortunately, aquaculture-related microbiome studies are scarce in Southeast Asia countries despite the severe impact of early mortality syndrome outbreaks on shrimp production in the region. In this study, we employed the 16S rRNA amplicon (V3–V4 region) sequencing and amplicon sequence variants (ASV) method to investigate the microbial diversity of shrimp guts and pond water samples collected from aquaculture farms located in Malaysia and Vietnam. Substantial differences in the pond microbiota were observed between countries with the presence and absence of several taxa extending to the family level. Microbial diversity of the shrimp gut was found to be generally lower than that of the pond environments with a few ubiquitous genera representing a majority of the shrimp gut microbial diversity such as Vibrio and Photobacterium, indicating host-specific selection of microbial species. Given the high sequence conservation of the 16S rRNA gene, we assessed its veracity at distinguishing Vibrio species based on nucleotide alignment against type strain reference sequences and demonstrated the utility of ASV approach in uncovering a wider diversity of Vibrio species compared to the conventional OTU clustering approach.
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Affiliation(s)
- Muhammad Zarul Hanifah Md Zoqratt
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Wilhelm Wei Han Eng
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia
| | - Binh Thanh Thai
- Fisheries and Technical, Economical College, Dinh Bang, Tu Son, Vietnam
| | - Christopher M Austin
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
| | - Han Ming Gan
- School of Science, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Selangor, Malaysia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia.,Centre for Integrative Ecology, School of Life and Environmental Sciences, Deakin University, Geelong, Victoria, Australia
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14
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Black EM, Chimenti MS, Just CL. Metagenomic analysis of nitrogen-cycling genes in upper Mississippi river sediment with mussel assemblages. Microbiologyopen 2018; 8:e00739. [PMID: 30270525 PMCID: PMC6528593 DOI: 10.1002/mbo3.739] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 08/20/2018] [Accepted: 08/28/2018] [Indexed: 11/30/2022] Open
Abstract
We investigated the impact of native freshwater mussel assemblages (order Unionoida) on the abundance and composition of nitrogen‐cycling genes in sediment of an upper Mississippi river habitat. We hypothesized that the genomic potential for ammonia and nitrite oxidation would be greater in the sediment with mussel assemblages, presumably due to mussel biodeposition products, namely ammonia and organic carbon. Regardless of the presence of mussels, upper Mississippi river sediment microbial communities had the largest genomic potential for nitrogen fixation followed by urea catabolism, nitrate metabolism, and nitrate assimilation, as evidenced by analysis of nitrogen cycling pathway abundances. However, genes encoding nitrate and nitrite redox reactions, narGHI and nxrAB, were the most abundant functional genes of the nitrogen cycling gene families. Using linear discriminant analysis (LDA), we found nitrification genes were the most important biomarkers for nitrogen cycling genomic potential when mussels were present, and this presented an opposing effect on the abundance of genes encoding nitric oxide reduction. The genes involved in nitrification that increased the most were amoA associated with comammox Nitrospira and nxr homologs associated with Nitrospira. On the other hand, the most distinctive biomarkers of microbial communities without mussels were norB and nrfA, as part of denitrification and dissimilatory nitrate reduction to ammonium pathways, respectively. Ultimately, this research demonstrates the impact of native mollusks on microbial nitrogen cycling in an aquatic agroecosystem.
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Affiliation(s)
- Ellen M Black
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, Iowa
| | - Michael S Chimenti
- Iowa Institute of Human Genetics, Carver College of Medicine, University of Iowa, Iowa City, Iowa
| | - Craig L Just
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, Iowa
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15
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Black EM, Just CL. The Genomic Potentials of NOB and Comammox Nitrospira in River Sediment Are Impacted by Native Freshwater Mussels. Front Microbiol 2018; 9:2061. [PMID: 30233538 PMCID: PMC6131200 DOI: 10.3389/fmicb.2018.02061] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/13/2018] [Indexed: 11/24/2022] Open
Abstract
Freshwater mussel assemblages of the Upper Mississippi River (UMR) sequester tons of ammonia- and urea-based biodeposits each day and aerate sediment through burrowing activities, thus creating a unique niche for nitrogen (N) cycling microorganisms. This study explored how mussels impact the abundance of N-cycling species with an emphasis on Candidatus Nitrospira inopinata, the first microorganism known to completely oxidize ammonia (comammox) to nitrate. This study used metagenomic shotgun sequencing of genomic DNA to compare nitrogen cycling species in sediment under a well-established mussel assemblage and in nearby sediment without mussels. Metagenomic reads were aligned to the prokaryotic RefSeq non-redundant protein database using BLASTx, taxonomic binning was performed using the weighted lowest common ancestor algorithm, and protein-coding genes were categorized by metabolic function using the SEED subsystem. Linear discriminant analysis (LDA) effect sizes were used to determine which metagenomes and metabolic features explained the most differences between the mussel habitat sediment and sediment without mussels. Of the N-cycling species deemed differentially abundant, Nitrospira moscoviensis and “Candidatus Nitrospira inopinata” were responsible for creating a distinctive N-cycling microbiome in the mussel habitat sediment. Further investigation revealed that comammox Nitrospira had a large metabolic potential to degrade mussel biodeposits, as evidenced the top ten percent of protein-coding genes including the cytochrome c-type biogenesis protein required for hydroxylamine oxidation, ammonia monooxygenase, and urea decomposition SEED subsystems. Genetic marker analysis of these two Nitrospira taxons suggested that N. moscoviensis was most impacted by diverse carbon metabolic processes while “Candidatus Nitrospira inopinata” was most distinguished by multidrug efflux proteins (AcrB), NiFe hydrogenase (HypF) used in hydrogen oxidation and sulfur reduction coupled reactions, and a heme chaperone (CcmE). Furthermore, our research suggests that comammox and NOB Nitrospira likely coexisted by utilizing mixotrophic metabolisms. For example, “Candidatus Nitrospira inopinata” had the largest potentials for ammonia oxidation, nitrite reduction with NirK, and hydrogen oxidation, while NOB Nitrospira had the greatest potential for nitrite oxidation, and nitrate reduction possibly coupled with formate oxidation. Overall, our results suggest that this mussel habitat sediment harbors a niche for NOB and comammox Nitrospira, and ultimately impacts N-cycling in backwaters of the UMR.
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Affiliation(s)
- Ellen M Black
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA, United States
| | - Craig L Just
- Department of Civil and Environmental Engineering, University of Iowa, Iowa City, IA, United States
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16
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Aldhafiri S, Mahmoud H, Al-Sarawi M, Ismail WA. Natural Attenuation Potential of Polychlorinated Biphenyl-Polluted Marine Sediments. Pol J Microbiol 2018; 67:37-48. [DOI: 10.5604/01.3001.0011.6140] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2017] [Indexed: 12/23/2022] Open
Abstract
The marine environment in Kuwait is polluted with various hazardous chemicals of industrial origin. These include petroleum hydrocarbons, halogenated compounds and heavy metals. Bioremediation with dedicated microorganisms can be effectively applied for reclamation of the polluted marine sediments. However, information on the autochthonous microbes and their ecophysiology is largely lacking. We analyzed sediments from Shuwaikh harbor to detect polychlorinated biphenyls (PCBs) and total petroleum hydrocarbons (TPHs). Then we adopted both culture-dependent and culture-independent (PCR-DGGE) approaches to identify bacterial inhabitants of the polluted marine sediments from Shuwaikh harbor. The chemical analysis revealed spatial variation among the sampling stations in terms of total amount of PCBs, TPHs and the PCB congener fingerprints. Moreover, in all analyzed sediments, the medium-chlorine PCB congeners were more abundant than the low-chlorine and high-chlorine counterparts. PCR-DGGE showed the presence of members of the Proteobacteria, Spirochaetes, Firmicutes and Bacteroidetes in the analyzed sediments. However, Chloroflexi-related bacteria dominated the detected bacterial community. We also enriched a biphenyl-utilizing mixed culture using the W2 station sediment as an inoculum in chemically defined medium using biphenyl as a sole carbon and energy source. The enriched mixed culture consisted mainly of the Firmicute Paenibacillus spp. Sequences of genes encoding putative aromatic ring-hydroxylating dioxygenases were detected in sediments from most sampling stations and the enriched mixed culture. The results suggest the potential of bioremediation as a means for natural attenuation of Shuwaikh harbor sediments polluted with PCBs and TPHs.
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Affiliation(s)
- Sarah Aldhafiri
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
| | - Huda Mahmoud
- Department of Biological Sciences, College of Science, Kuwait University, Kuwait
| | - Mohammed Al-Sarawi
- Department of Earth and Environmental Sciences, College of Science, Kuwait University, Kuwait
| | - Wael A. Ismail
- Environmental Biotechnology Program, Life Sciences Department, College of Graduate Studies, Arabian Gulf University, Manama, Kingdom of Bahrain
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17
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Arshad A, Dalcin Martins P, Frank J, Jetten MSM, Op den Camp HJM, Welte CU. Mimicking microbial interactions under nitrate-reducing conditions in an anoxic bioreactor: enrichment of novel Nitrospirae bacteria distantly related to Thermodesulfovibrio. Environ Microbiol 2017; 19:4965-4977. [PMID: 29105249 DOI: 10.1111/1462-2920.13977] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/26/2017] [Accepted: 10/28/2017] [Indexed: 11/29/2022]
Abstract
Microorganisms are main drivers of the sulfur, nitrogen and carbon biogeochemical cycles. These elemental cycles are interconnected by the activity of different guilds in sediments or wastewater treatment systems. Here, we investigated a nitrate-reducing microbial community in a laboratory-scale bioreactor model that closely mimicked estuary or brackish sediment conditions. The bioreactor simultaneously consumed sulfide, methane and ammonium at the expense of nitrate. Ammonium oxidation occurred solely by the activity of anammox bacteria identified as Candidatus Scalindua brodae and Ca. Kuenenia stuttgartiensis. Fifty-three percent of methane oxidation was catalyzed by archaea affiliated to Ca. Methanoperedens and 47% by Ca. Methylomirabilis bacteria. Sulfide oxidation was mainly shared between two proteobacterial groups. Interestingly, competition for nitrate did not lead to exclusion of one particular group. Metagenomic analysis showed that the most abundant taxonomic group was distantly related to Thermodesulfovibrio sp. (87-89% 16S rRNA gene identity, 52-54% average amino acid identity), representing a new family within the Nitrospirae phylum. A high quality draft genome of the new species was recovered, and analysis showed high metabolic versatility. Related microbial groups are found in diverse environments with sulfur, nitrogen and methane cycling, indicating that these novel Nitrospirae bacteria might contribute to biogeochemical cycling in natural habitats.
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Affiliation(s)
- Arslan Arshad
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | | | - Jeroen Frank
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.,Soehngen Institute for Anaerobic Microbiology, Radboud University, Nijmegen, The Netherlands
| | - Mike S M Jetten
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.,Soehngen Institute for Anaerobic Microbiology, Radboud University, Nijmegen, The Netherlands.,Netherlands Earth Systems Science Center, Utrecht University, Utrecht, The Netherlands
| | - Huub J M Op den Camp
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands
| | - Cornelia U Welte
- Department of Microbiology, Institute for Water and Wetland Research, Radboud University, Nijmegen, The Netherlands.,Soehngen Institute for Anaerobic Microbiology, Radboud University, Nijmegen, The Netherlands
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