51
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Brindefalk B, Brolin H, Säve‐Söderbergh M, Karlsson E, Sundell D, Wikström P, Jacobsson K, Toljander J, Stenberg P, Sjödin A, Dryselius R, Forsman M, Ahlinder J. Bacterial composition in Swedish raw drinking water reveals three major interacting ubiquitous metacommunities. Microbiologyopen 2022; 11:e1320. [PMID: 36314747 PMCID: PMC9511821 DOI: 10.1002/mbo3.1320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/10/2022] [Accepted: 09/10/2022] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Surface raw water used as a source for drinking water production is a critical resource, sensitive to contamination. We conducted a study on Swedish raw water sources, aiming to identify mutually co-occurring metacommunities of bacteria, and environmental factors driving such patterns. METHODS The water sources were different regarding nutrient composition, water quality, and climate characteristics, and displayed various degrees of anthropogenic impact. Water inlet samples were collected at six drinking water treatment plants over 3 years, totaling 230 samples. The bacterial communities of DNA sequenced samples (n = 175), obtained by 16S metabarcoding, were analyzed using a joint model for taxa abundance. RESULTS Two major groups of well-defined metacommunities of microorganisms were identified, in addition to a third, less distinct, and taxonomically more diverse group. These three metacommunities showed various associations to the measured environmental data. Predictions for the well-defined metacommunities revealed differing sets of favored metabolic pathways and life strategies. In one community, taxa with methanogenic metabolism were common, while a second community was dominated by taxa with carbohydrate and lipid-focused metabolism. CONCLUSION The identification of ubiquitous persistent co-occurring bacterial metacommunities in freshwater habitats could potentially facilitate microbial source tracking analysis of contamination issues in freshwater sources.
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Affiliation(s)
- Björn Brindefalk
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Harald Brolin
- Department of Molecular and Clinical Medicine, Institute of Medicine, Sahlgrenska AcademyUniversity of GothenburgGothenburgSweden
| | - Melle Säve‐Söderbergh
- Science DivisionSwedish Food AgencyUppsalaSweden
- Institute of Environmental Medicine, Karolinska InstitutetStockholmSweden
| | - Edvin Karlsson
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
- Department of Ecology and Environmental Science (EMG)Umeå UniversityUmeåSweden
| | - David Sundell
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Per Wikström
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Karin Jacobsson
- Department of Biomedical Science and Veterinary Public HealthSwedish University of Agricultural SciencesUppsalaSweden
| | | | - Per Stenberg
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
- Department of Ecology and Environmental Science (EMG)Umeå UniversityUmeåSweden
| | - Andreas Sjödin
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | | | - Mats Forsman
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
| | - Jon Ahlinder
- CBRN Security and Defence, FOI, Swedish Defence Research AgencyUmeåSweden
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52
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Zhao RZ, Zhang WJ, Zhang W, Zhao ZF, Qiu XC. A Preliminary Study of Bacterioplankton Community Structure in the Taiyangshan Wetland in Ningxia and Its Driving Factors. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:12224. [PMID: 36231526 PMCID: PMC9565018 DOI: 10.3390/ijerph191912224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
The Taiyangshan Wetland, a valuable wetland resource in the arid zone of central Ningxia, is critical for flood storage and drought resistance, climate regulation, and biodiversity protection. Nevertheless, the community structure and diversity of bacterioplankton in the Taiyangshan Wetland remains unclear. High-throughput sequencing was used to analyze the differences in bacterioplankton structure and major determinants in the Taiyangshan Wetland from April to October 2020. The composition and diversity of the bacterioplankton community varied significantly in different sampling periods but showed negligible differences across lake regions. Meanwhile, the relative abundances of bacterioplankton Bacteroidetes, Actinobacteria, Firmicutes, Chloroflexi, Tenericutes, Epsilonbacteraeota, and Patescibacteria were significantly different in different sampling periods, while the relative abundances of Cyanobacteria in different lake regions were quite different. Network analysis revealed that the topological attributes of co-occurrence pattern networks of bacterioplankton were high, and bacterioplankton community compositions were complicated in the month of July. A mantel test revealed that the bacterioplankton community in the entire wetland was affected by water temperature, electrical conductivity, dissolved oxygen, salinity, total nitrogen, ammonia nitrogen, chemical oxygen demand, fluoride, and sulfate. The bacterioplankton community structure was affected by ten environmental parameters (e.g., water temperature, dissolved oxygen, salinity, and permanganate index) in April, while the bacterioplankton community was only related to 1~2 environmental parameters in July and October. The bacterioplankton community structure in Lake Region IV was related to seven environmental parameters, including dissolved oxygen, pH, total nitrogen, and chemical oxygen demand, whereas the bacterioplankton community structures in the other three lake regions were related to two environmental parameters. This study facilitates the understanding of the bacterioplankton community in wetlands in arid areas and provides references to the evaluation of aquatic ecological management of the Taiyangshan Wetland.
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Affiliation(s)
- Rui-Zhi Zhao
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Wei-Jiang Zhang
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Wen Zhang
- Ningxia Supervision Institute for Veterinary Drugs and Animal Feedstuffs, Yinchuan 750004, China
| | - Zeng-Feng Zhao
- School of Civil and Hydraulic Engineering, Ningxia University, Yinchuan 750021, China
| | - Xiao-Cong Qiu
- School of Life Science, Ningxia University, Yinchuan 750021, China
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53
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Zufiaurre A, Felip M, Camarero L, Sala-Faig M, Juhanson J, Bonilla-Rosso G, Hallin S, Catalan J. Bacterioplankton seasonality in deep high-mountain lakes. Front Microbiol 2022; 13:935378. [PMID: 36187988 PMCID: PMC9519062 DOI: 10.3389/fmicb.2022.935378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/08/2022] [Indexed: 12/04/2022] Open
Abstract
Due to global warming, shorter ice cover duration might drastically affect the ecology of lakes currently undergoing seasonal surface freezing. High-mountain lakes show snow-rich ice covers that determine contrasting conditions between ice-off and ice-on periods. We characterized the bacterioplankton seasonality in a deep high-mountain lake ice-covered for half a year. The lake shows a rich core bacterioplankton community consisting of three components: (i) an assemblage stable throughout the year, dominated by Actinobacteria, resistant to all environmental conditions; (ii) an ice-on-resilient assemblage dominating during the ice-covered period, which is more diverse than the other components and includes a high abundance of Verrucomicrobia; the deep hypolimnion constitutes a refuge for many of the typical under-ice taxa, many of which recover quickly during autumn mixing; and (iii) an ice-off-resilient assemblage, which members peak in summer in epilimnetic waters when the rest decline, characterized by a dominance of Flavobacterium, and Limnohabitans. The rich core community and low random elements compared to other relatively small cold lakes can be attributed to its simple hydrological network in a poorly-vegetated catchment, the long water-residence time (ca. 4 years), and the long ice-cover duration; features common to many headwater deep high-mountain lakes.
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Affiliation(s)
- Aitziber Zufiaurre
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Área de Biodiversidad, Gestión ambiental de Navarra-Nafarroako Ingurumenkudeaketa (GAN-NIK), Pamplona-Iruñea, Navarra, Spain
| | - Marisol Felip
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- Departament de Biologia Evolutiva, Ecologia i Ciències Ambientals, Universitat de Barcelona, Barcelona, Catalonia, Spain
| | - Lluís Camarero
- Centre d’Estudis Avançats de Blanes (CEAB), CSIC, Blanes, Catalonia, Spain
| | - Marc Sala-Faig
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
| | - Jaanis Juhanson
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - German Bonilla-Rosso
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Sara Hallin
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jordi Catalan
- CREAF, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
- CSIC, Cerdanyola del Vallès, Barcelona, Catalonia, Spain
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54
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Lian S, Qu Y, Dai C, Li S, Jing J, Sun L, Yang Y. Succession of function, assembly, and interaction of microbial community in sequencing biofilm batch reactors under selenite stress. ENVIRONMENTAL RESEARCH 2022; 212:113605. [PMID: 35660567 DOI: 10.1016/j.envres.2022.113605] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
The mechanism of interaction between selenite, a toxic substance, and the microbial community in wastewater is still not well understood. Herein, nine sequencing biofilm batch reactors were used to systematically investigate the response of the microbial community to the continuous selenite stress. The results showed that selenite affected the reactor performance and reduced the biofilm mass. Also, it increased the proportion of the living cells, and changed the protein and polysaccharide composition of the biofilm as well as cellular secretions. Selenite facilitated the removal of NO3-N, according to water-quality and bioinformatics analyses. As such, the selenite was converted into selenium nanoparticles. α-diversity analysis further revealed that 20 μM selenite enhanced the microbial community resilience, while 200 μM selenite had the reverse effect. Community composition analysis showed that Variovorax, Rhizobium, and Simkania had positive correlations with selenite (P < 0.05). Functional prediction suggested that selenite changed the C, N, and S cycle functions. Furthermore, determinism dominated the community assembly process, and the deterministic proportion increased with the increase of selenite concentration. Network analysis showed that selenite improved the stability and positive correlation ratio of the overall microbial network, and accelerated the communication between microorganisms. However, when compared with the 20 μM selenite, the 200 μM selenite boosted the competition and parasitism/predation among microorganisms. Low-abundance genera played a key role in the network of selenite-reducing microbial community. In addition, under selenite stress, biofilm network exhibited better stability and faster information exchange than suspended network, and the positive association between biofilm and suspended microorganisms increased. All in all, this research sheds light on the interaction between selenite and microbial community, as well as provides crucial information on selenium-containing wastewater.
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Affiliation(s)
- Shengyang Lian
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Yuanyuan Qu
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China.
| | - Chunxiao Dai
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Shuzhen Li
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Jiawei Jing
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Lu Sun
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Ying Yang
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
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55
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Yuan AE, Shou W. Data-driven causal analysis of observational biological time series. eLife 2022; 11:e72518. [PMID: 35983746 PMCID: PMC9391047 DOI: 10.7554/elife.72518] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 01/23/2022] [Indexed: 11/28/2022] Open
Abstract
Complex systems are challenging to understand, especially when they defy manipulative experiments for practical or ethical reasons. Several fields have developed parallel approaches to infer causal relations from observational time series. Yet, these methods are easy to misunderstand and often controversial. Here, we provide an accessible and critical review of three statistical causal discovery approaches (pairwise correlation, Granger causality, and state space reconstruction), using examples inspired by ecological processes. For each approach, we ask what it tests for, what causal statement it might imply, and when it could lead us astray. We devise new ways of visualizing key concepts, describe some novel pathologies of existing methods, and point out how so-called 'model-free' causality tests are not assumption-free. We hope that our synthesis will facilitate thoughtful application of methods, promote communication across different fields, and encourage explicit statements of assumptions. A video walkthrough is available (Video 1 or https://youtu.be/AIV0ttQrjK8).
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Affiliation(s)
- Alex Eric Yuan
- Molecular and Cellular Biology PhD program, University of WashingtonSeattleUnited States
- Basic Sciences Division, Fred Hutchinson Cancer Research CenterSeattleUnited States
| | - Wenying Shou
- Centre for Life’s Origins and Evolution, Department of Genetics, Evolution and Environment, University College LondonLondonUnited Kingdom
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56
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Mao W, Yang R, Shi H, Feng H, Chen S, Wang X. Identification of key water parameters and microbiological compositions triggering intensive N 2O emissions during landfill leachate treatment process. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155135. [PMID: 35405234 DOI: 10.1016/j.scitotenv.2022.155135] [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: 12/15/2021] [Revised: 03/16/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Landfill leachate treatment processes tend to emit more N2O compared to domestic wastewater treatment. This discrepancy may be ascribed to leachate water characteristics such as high refractory COD, ammonium (NH4+) content, and salinity. In this work, the leachate influent was varied to examine the N2O emission scenarios. NH4+-N, COD, and Cl- concentrations ranged between 1000-2500, 1000-10,000, and 500-3000 mg L-1, respectively. Simultaneously, we attempted to combine statistical analysis with high-throughput sequencing to understand the microbial mechanism with regards to N2O emission. Results show that the strong N2O emissions occur in the nitrifying tank due to the intensive aeration. The system receiving the lowest COD shows the maximum N2O emission factor of 42.7% of the removed nitrogen. Both redundancy analysis and a structural equation model verify that insufficient degradable organics are the key water parameter triggering intensive N2O emission within the designed influent limits. Furthermore, two essential but non-abundant functional bacteria, Flavobacterium (acting as a denitrifier) and Nitrosomonas (acting as a nitrifier), are identified as the core functional species that dramatically influence N2O emissions. An increase in influent COD promotes the proliferation of Flavobacterium and inhibits Nitrosomonas, which in turn reduce N2O release. Meanwhile, two keystone species of Castellaniella and Saprospiraceae unclassified are recognized. They may supply a suitable niche and integrity of the microbial community for N-cycle functional bacteria. These findings reveal the essential role of non-abundant species in microbial community, and expand the current understanding of microbial interactions underlying N2O dynamics in leachate treatment systems.
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Affiliation(s)
- Wenlong Mao
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Ruili Yang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Huiqun Shi
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
| | - Hualiang Feng
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Shaohua Chen
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
| | - Xiaojun Wang
- Key Laboratory of Urban Pollutant Conversion, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.
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57
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Mikhailov IS, Galachyants YP, Bukin YS, Petrova DP, Bashenkhaeva MV, Sakirko MV, Blinov VV, Titova LA, Zakharova YR, Likhoshway YV. Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal. MICROBIAL ECOLOGY 2022; 84:404-422. [PMID: 34510242 DOI: 10.1007/s00248-021-01860-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs). Individual OTUs were consistently replaced during different seasonal events. The coherent clusters change their contribution to the microbial community depending on season. Changes of temperature, concentrations of silicon, and nitrates are the key factors affected the structure of microbial communities. Functional prediction revealed that some bacterial or eukaryotic taxa that switched with seasons had similar functional properties, which demonstrate their functional redundancy. We have also detected specific functional properties in different coherent clusters of bacteria or microeukaryotes, which can indicate their ability to adapt to seasonal changes of environment. Our results revealed a relationship between seasonal succession, coherency, and functional features of freshwater bacteria and microeukaryotes.
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Affiliation(s)
- Ivan S Mikhailov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia.
| | - Yuri P Galachyants
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yuri S Bukin
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Darya P Petrova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Bashenkhaeva
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Maria V Sakirko
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Vadim V Blinov
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Lubov A Titova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yulia R Zakharova
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
| | - Yelena V Likhoshway
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Irkutsk, Russia
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58
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Wang X, Wu H, Dai C, Wang X, Wang L, Xu J, Lu Z. Microbial interactions enhanced environmental fitness and expanded ecological niches under dibutyl phthalate and cadmium co-contamination. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119362. [PMID: 35489538 DOI: 10.1016/j.envpol.2022.119362] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/14/2022] [Accepted: 04/23/2022] [Indexed: 06/14/2023]
Abstract
Co-contamination of organic pollutants and heavy metals is universal in the natural environment. Dibutyl phthalate (DBP), a typical plasticizer, frequently coexists with cadmium (Cd) in nature. However, little attention has been given to the impacts of co-contamination by DBP and Cd on microbial communities or the responses of microbes. To address this, a microcosm experiment was conducted by supplying the exogenous DBP-degrading bacterium Glutamicibacter nicotianae ZM05 to investigate the interplay among DBP-Cd co-contamination, the exogenous DBP-degrading bacterium G. nicotianae ZM05, and indigenous microorganisms. To adapt to co-contamination stress, microbial communities adjust their diversity, interactions, and functions. The stability of the microbial community decreased under co-contamination, as evidenced by lower diversity, simpler network, and fewer ecological niches. Microbial interactions were strengthened, as evidenced by enriched pathways related to microbial communications. Meanwhile, interactions between microorganisms enhanced the environmental fitness of the exogenous DBP-degrading bacterium ZM05. Based on co-occurrence network prediction and coculture experiments, metabolic interactions between the non-DBP-degrading bacterium Cupriavidus metallidurans ZM16 and ZM05 were proven. Strain ZM16 utilized protocatechuic acid, a DBP downstream metabolite, to relieve acid inhibition and adsorbed Cd to relieve toxic stress. These findings help to explain the responses of bacterial and fungal communities to DBP-Cd co-contamination and provide new insights for the construction of degrading consortia for bioremediation.
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Affiliation(s)
- Xuejun Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hao Wu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chuhan Dai
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaoyu Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Lvjing Wang
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Zhenmei Lu
- MOE Laboratory of Biosystem Homeostasis and Protection, College of Life Sciences, Zhejiang University, Hangzhou, China.
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59
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Wu H, Zhang Z, Wang J, Qin X, Chen J, Wu L, Lin S, Rensing C, Lin W. Bio-fertilizer Amendment Alleviates the Replanting Disease under Consecutive Monoculture Regimes by Reshaping Leaf and Root Microbiome. MICROBIAL ECOLOGY 2022; 84:452-464. [PMID: 34554283 DOI: 10.1007/s00248-021-01861-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 09/02/2021] [Indexed: 06/13/2023]
Abstract
Replanting disease is a growing problem in intensive agricultural systems. Application of bio-fertilizer containing beneficial microbes contributes to disease suppression and is a promising strategy to control replanting disease. However, the effect of both replanting disease and bio-fertilizer amendment on the assembly of crop microbiota in leaves and roots and their relationships to crop yield and quality remains elusive. In these experiments, roots and leaves of Radix pseudostellariae were collected from different consecutive monoculture and bio-fertilizer amended fields, and the associated microbiota were characterized by bacterial 16S rRNA gene sequencing and quantitative PCR. Consecutive monoculture altered the bacterial community structure and composition and significantly increased the abundance of potential pathogenic Ralstonia and Fusarium oxysporum in leaves and roots. Furthermore, bio-fertilizer application alleviated replanting disease by decreasing the pathogen load, increasing the potential beneficial genera Pseudomonas, Streptomyces, Paenibacillus, and Bradyrhizobium. The proportion of positive correlations in the co-occurrence network of bio-fertilizer application was the highest, implying that bio-fertilizer potentially enhanced ecological commensalism or mutualism of the bacterial community across the two compartments. Structural equation models indicated that bio-fertilizer had a positive and indirect effect on both yield and quality by shaping the leaf microbiota and the root microbiota. Our findings highlight the role of leaf and root microbiota on replanting disease, showing that bio-fertilizer contributes to alleviating replanting disease by improving microbe-microbe interactions.
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Affiliation(s)
- Hongmiao Wu
- Laboratory of Rhizosphere Ecology Processes and Management, College of Resource and Environment, Anhui Agricultural University, Hefei, 230036, People's Republic of China
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Zhen Zhang
- Laboratory of Rhizosphere Ecology Processes and Management, College of Resource and Environment, Anhui Agricultural University, Hefei, 230036, People's Republic of China.
| | - Juanying Wang
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Xianjin Qin
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Jun Chen
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Linkun Wu
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Sheng Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China
| | - Christopher Rensing
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
| | - Wenxiong Lin
- Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
- Key Laboratory for Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education/College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, People's Republic of China.
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60
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Interkingdom Plant–Soil Microbial Ecological Network Analysis under Different Anthropogenic Impacts in a Tropical Rainforest. FORESTS 2022. [DOI: 10.3390/f13081167] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Plants and their associated soil microorganisms interact with each other and form complex relationships. The effects of slash-and-burn agriculture and logging on aboveground plants and belowground microorganisms have been extensively studied, but research on plant–microbial interkingdom ecological networks is lacking. In this study, using old growth forest as a control, we used metagenomic data (ITS and 16S rRNA gene amplified sequences) and plant data to obtain interdomain species association patterns for three different soil disturbance types (slash-and-burn, clear cutting and selective cutting) in a tropical rainforest based on interdomain ecological network (IDEN) analysis. Results showed that the soil bacterial–fungal and plant–microbe ecological networks had different topological properties among the three forest disturbance types compared to old growth forest. More nodes, links, higher modularity and negative proportion were found in the selective cutting stand, indicating higher stability with increasing antagonistic relationships and niche differentiation. However, the area of slash-and-burn forest yield opposite results. Network module analysis indicated that different keystone species were found in the four forest types, suggesting alternative stable states among them. Different plant species had more preferential associations with specific fungal taxa than bacterial taxa at the genus level and plant–microbe associations lagged behind bacterial–fungal associations. Overall, compared with old growth forests, the bacterial–fungal and plant–microbe ecological networks in the slash-and-burn and clear cutting stands were simpler, while the network in the selective cutting stand was more complex. Understanding the relationships between aboveground plants and belowground microorganisms under differing disturbance patterns in natural ecosystems will help in better understanding the surrounding ecosystem functions of ecological networks.
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Xu L, Xiang P, Zhang B, Yang K, Liu F, Wang Z, Jin Y, Deng L, Gan W, Song Z. Host Species Influence the Gut Microbiota of Endemic Cold-Water Fish in Upper Yangtze River. Front Microbiol 2022; 13:906299. [PMID: 35923412 PMCID: PMC9339683 DOI: 10.3389/fmicb.2022.906299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/22/2022] [Indexed: 11/28/2022] Open
Abstract
The fish gut microbiome plays an important role in nutrition absorption and energy metabolism. Studying the gut microbes of cold-water fish is important to understand the dietary adaptation strategies in extreme environments. In this study, the gut samples of Schizothorax wangchiachii (SW, herbivorous), Schizothorax kozlovi (SK, omnivorous), and Percocypris pingi (PP, carnivorous) in the upper Yangtze River were collected, and we sequenced 16S rRNA amplicon to study the potential relationship between gut microbes and host species. The results showed that gut microbial composition and diversity were significantly different between the three cold-water fishes. These fishes had different key taxa in their gut microbes, including bacteria involved in the breakdown of food (e.g., Cetobacterium, Aeromonas, and Clostridium sensu stricto 10). The highest alpha diversity indices (e.g., Chao 1 index) were identified in the herbivore (SW), followed by the carnivore (PP), and the lowest in the omnivore (SK). Non-metric multidimensional scaling (NMDS) results revealed that the gut microbial community of these species was different between host species. The neutral community model (NCM) showed that the microbial community structure of SW was shaped by stochastic processes, and the highest species dispersal was found in SW, followed by PP, and the lowest in SK. The results of niche breadth agreed with these findings. Our results demonstrated that host species influenced the gut microbiome composition, diversity, and microbial community assembly processes of the three cold-water fishes. These findings implied that the variation of gut microbiome composition and function plays a key role in digesting and absorbing nutrients from different foods in cold-water fish.
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Affiliation(s)
- Liangliang Xu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Peng Xiang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Baowen Zhang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Kun Yang
- Institute of Ecology, China West Normal University, Nanchong, China
| | - Fenglin Liu
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zesong Wang
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yanjun Jin
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
| | - Longjun Deng
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Weixiong Gan
- Yalong River Hydropower Development Company, Ltd., Chengdu, China
| | - Zhaobin Song
- Key Laboratory of Bio-Resources and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Observation and Research Station of Sichuan Province of Fish Resources and Environment in Upper Reaches of the Yangtze River, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Zhaobin Song,
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Yuan S, Guo S, Huang X, Meng F. Time-lagged interspecies interactions prevail during biofilm development in moving bed biofilm reactor. Biotechnol Bioeng 2022; 119:2770-2783. [PMID: 35837838 DOI: 10.1002/bit.28177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/27/2022] [Accepted: 07/10/2022] [Indexed: 11/09/2022]
Abstract
Clarifying the essential succession dynamics of interspecies interactions during biofilm development is crucial for the regulation and application of biofilm-based processes. In this study, regular and time-series phylogenetic molecular ecological networks (pMENs) were constructed to investigate ordinary and time-lagged interspecies interactions during biofilm development in a moving bed biofilm reactor (MBBR). Positive interactions dominated both regular (89.78%) and time-series (77.04%) ecological networks, suggesting that extensive cooperative behaviors facilitated biofilm development. The pronounced directional interactions (72.52%) in the time-series network further indicated that time-lagged interspecies interactions prevailed in the biofilm development process. Specifically, the proportion of directional negative interactions was higher than that of positive interactions, implying that interspecific competition preferred to be time-lagged. The time-series network revealed that module hubs exhibited extensive time-lagged positive interactions with their neighbors, and most of them exhibited altruistic behaviors. Keystone species possessing more positive interactions were positively correlated with biofilm biomass, NO3 - -N concentrations, and the removal efficiencies of NH4 + -N and COD. However, keystone species and peripherals that were negatively targeted by their neighbors showed positive correlations with the concentrations of NO2 - -N, polysaccharides, and proteins in the soluble microbial products. The data highlight that the time-series network can provide directional microbial interactions along with the biofilm development process, which would help to predict the tendency of community shifts and propose efficient strategies for the regulation of biofilm-based processes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Shasha Yuan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Sixian Guo
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Xihao Huang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, PR China.,Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, (Sun Yat-sen University), Guangzhou, 510275, PR China
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63
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Xia F, Liu Z, Zhao M, Li Q, Li D, Cao W, Zeng C, Hu Y, Chen B, Bao Q, Zhang Y, He Q, Lai C, He X, Ma Z, Han Y, He H. High stability of autochthonous dissolved organic matter in karst aquatic ecosystems: Evidence from fluorescence. WATER RESEARCH 2022; 220:118723. [PMID: 35696806 DOI: 10.1016/j.watres.2022.118723] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/20/2022] [Accepted: 06/06/2022] [Indexed: 05/26/2023]
Abstract
Biological carbon pump (BCP) in karst areas has received intensive attention for years due to their significant contribution to the global missing carbon sink. The stability of autochthonous dissolved organic matter (Auto-DOM) produced by BCP in karst aquatic ecosystems may play a critical role in the missing carbon sink. However, the source of dissolved organic matter (DOM) in inland waters and its consumption by planktonic bacteria have not been thoroughly examined. Recalcitrant dissolved organic matter (RDOM) may exist in karst aquatic ecosystem as in the ocean. Through the study of the chromophoric dissolved organic matter (CDOM) and the interaction between CDOM and the planktonic bacterial community under different land uses at the Shawan Karst Water-carbon Cycle Test Site, SW China, we found that C2, as the fluorescence component of Auto-DOM mineralised by planktonic bacteria, may have some of the characteristics of RDOM and is an important DOM source in karst aquatic ecosystems. The stability ratio (Fmax(C2/(C1+C2))) of Auto-DOM reached 89.6 ± 6.71% in winter and 64.1 ± 7.19% in spring. Moreover, correlation-based network analysis determined that the planktonic bacterial communities were controlled by different fluorescence types of CDOM, of which C1 (fresh Auto-DOM), C3 (conventional allochthonous DOM (Allo-DOM)) and C4 (the Allo-DOM mineralised by bacteria) were clustered in one module together with prevalent organic-degrading planktonic bacteria; C2 was clustered in another tightly combined module, suggesting specific microbial utilization strategies for the C2 component. In addition, some important planktonic bacterium and functional genes (including chemotrophic heterotrophs and photosynthetic bacteria) were found to be affected by high Ca2+ and dissolved inorganic carbon (DIC) concentrations in karst aquatic ecosystems. Our research showed that Auto-DOM may be as an important carbon sink as the Allo-DOM in karst ecosystems, the former generally being neglected based on a posit that it is easily and first mineralized by planktonic bacteria.
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Affiliation(s)
- Fan Xia
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Zaihua Liu
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China; CAS Center for Excellence in Quaternary Science and Global Change, Xi'an 710061, China.
| | - Min Zhao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Qiang Li
- Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Dong Li
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenfang Cao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
| | - Cheng Zeng
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Yundi Hu
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Bo Chen
- Guizhou University of Finance and Economics, Guiyang 550025, China
| | - Qian Bao
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; Key Laboratory of Land Resources Evaluation and Monitoring in Southwest China of Ministry of Education, Sichuan Normal University, Chengdu 610066, China
| | - Yi Zhang
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Resources and Environmental Engineering, Guizhou Institute of Technology, Guiyang 550008, China
| | - Qiufang He
- Chongqing Key Laboratory of Karst Environment, School of Geographical Sciences, Southwest University, Chongqing 400700, China; Key Laboratory of Karst Dynamics, Ministry of Nature Resources/Guangxi, Institute of Karst Geology, Chinese Academy of Geological Sciences, Guilin 541004, China
| | - Chaowei Lai
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing 100083, China
| | - Xuejun He
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Zhen Ma
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
| | - Yongqiang Han
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China; University of Chinese Academy of Sciences, Beijing 100049, China; Puding Karst Ecosystem Research Station, CAS, Chinese Ecosystem Research Network, Puding 562100, China
| | - Haibo He
- State Key Laboratory of Environmental Geochemistry, CAS, Institute of Geochemistry, Guiyang 550081, China
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Mohapatra M, Manu S, Dash SP, Rastogi G. Seagrasses and local environment control the bacterial community structure and carbon substrate utilization in brackish sediments. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 314:115013. [PMID: 35447445 DOI: 10.1016/j.jenvman.2022.115013] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/16/2022] [Accepted: 04/02/2022] [Indexed: 06/14/2023]
Abstract
Seagrasses are complex benthic coastal ecosystems that play a crucial role in organic matter cycling and carbon sequestration. However, little is known about how seagrasses influence the structure and carbon utilization potential of benthic bacterial communities. This study examined the bacterial communities in monospecific and mixed meadows of seagrasses and compared with bulk (unvegetated) sediments from Chilika, a brackish water coastal lagoon of India. High-throughput sequencing of 16S rRNA genes revealed a vegetation effect in terms of differences in benthic bacterial community diversity, composition, and abundances in comparison with bulk sediments. Desulfobacterales, Chromatiales, Enterobacteriales, Clostridiales, Vibrionales, and Acidimicrobiales were major taxa that contributed to differences between seagrass and bulk sediments. Seagrasses supported ∼5.94 fold higher bacterial abundances than the bulk due to rich organic carbon stock in their sediments. Co-occurrence network demonstrated much stronger potential interactions and connectedness in seagrass bacterial communities compared to bulk. Chromatiales and Acidimicrobiales were identified as the top two keystone taxa in seagrass bacterial communities, whereas, Dehalococcoidales and Rhizobiales were in bulk communities. Seagrasses and local environmental factors, namely, water depth, water pH, sediment salinity, redox potential, total organic carbon, available nitrogen, sediment texture, sediment pH, and sediment core depth were the major drivers of benthic bacterial community composition. Carbon metabolic profiling revealed that heterotrophic bacteria in seagrass sediments were much more metabolically diverse and active than bulk. The utilization of carbon substrate guilds, namely, amino acids, amines, carboxylic acids, carbohydrates, polymers, and phenolic compounds was enhanced in seagrass sediments. Metabolic mapping predicted higher prevalence of sulfate-reducer and N2 fixation metabolic functions in seagrass sediments. Overall, this study showed that seagrasses control benthic bacterial community composition and diversity, enhance heterotrophic carbon substrate utilization, and play crucial roles in organic matter cycling including degradation of hydrocarbon and xenobiotics in coastal sediments.
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Affiliation(s)
- Madhusmita Mohapatra
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India
| | - Shivakumara Manu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, 500048, India
| | - Stiti Prangya Dash
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India
| | - Gurdeep Rastogi
- Wetland Research and Training Centre, Chilika Development Authority, Balugaon, 752030, Odisha, India.
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Yang J, Wang S, Su W, Yu Q, Wang X, Han Q, Zheng Y, Qu J, Li X, Li H. Animal Activities of the Key Herbivore Plateau Pika ( Ochotona curzoniae) on the Qinghai-Tibetan Plateau Affect Grassland Microbial Networks and Ecosystem Functions. Front Microbiol 2022; 13:950811. [PMID: 35875528 PMCID: PMC9298508 DOI: 10.3389/fmicb.2022.950811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Plateau pikas (Ochotona curzoniae) are high-altitude model animals and famous "ecosystem engineers" on the Qinghai-Tibet Plateau. Pika activities may accelerate the degradation of alpine meadows. Nevertheless, little is known about the responses of bacterial, fungal, and archaeal communities, and ecosystem multifunctionality to pika perturbations. To address this question, we studied the impacts of only pika disturbance and combined disturbance (pika disturbance and grazing) on ecological networks of soil microbial communities and ecosystem multifunctionality. Our results demonstrated that Proteobacteria, Ascomycota, and Crenarchaeota were dominant in bacteria, fungi, and archaea, respectively. Bacteria, fungi, and archaea were all influenced by the combined disturbance of grazing and pika. Most fungal communities became convergent, while bacterial and archaeal communities became differentiated during the succession of surface types. In particular, the bacterial and fungal networks were less stable than archaeal networks. In response to the interference, cross-domain cooperation between bacterial and fungal communities increased, while competitive interactions between bacterial and archaeal communities increased. Pika disturbance at high intensity significantly reduced the ecosystem multifunctionality. However, the mixed effects of grazing and pika weakened such influences. This study revealed how pika activities affected microbial networks and ecosystem multifunctionality. These results provide insights to designing reasonable ecological management strategies for alpine grassland ecosystems.
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Affiliation(s)
- Jiawei Yang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Sijie Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Wanghong Su
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Qiaoling Yu
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Xiaochen Wang
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Qian Han
- School of Public Health, Lanzhou University, Lanzhou, China
| | - Yuting Zheng
- Changsha Central South Forestry Survey Planning and Design Co., Ltd., Changsha, China
| | - Jiapeng Qu
- Qinghai Provincial Key Laboratory of Restoration Ecology for Cold Region, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
| | - Xiangzhen Li
- Key Laboratory of Environmental and Applied Microbiology, Environmental Microbiology Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Huan Li
- School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, China
- State Key Laboratory of Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
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Ye Z, Wang J, Li J, Liu G, Dong Q, Zou Y, Chau HW, Zhang C. Different roles of core and noncore bacterial taxa in maintaining soil multinutrient cycling and microbial network stability in arid fertigation agroecosystems. J Appl Ecol 2022. [DOI: 10.1111/1365-2664.14228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Zhencheng Ye
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University Yangling P. R. China
| | - Jie Wang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University Yangling P. R. China
| | - Jing Li
- College of Forestry Northwest A&F University Yangling P. R. China
| | - Guobin Liu
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University Yangling P. R. China
- Institute of Soil and Water Conservation Chinese Academy of Sciences and Ministry of Water Resources Yangling P. R. China
| | - Qin’ge Dong
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University Yangling P. R. China
| | - Yufeng Zou
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas, Ministry of Education, Northwest A&F University Yangling China
| | - Henry Wai Chau
- Department of Soil and Physical Sciences Lincoln University Lincoln New Zealand
| | - Chao Zhang
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Northwest A&F University Yangling P. R. China
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Biological Microbial Interactions from Cooccurrence Networks in a High Mountain Lacustrine District. mSphere 2022; 7:e0091821. [PMID: 35642514 PMCID: PMC9241510 DOI: 10.1128/msphere.00918-21] [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
A fundamental question in biology is why some species tend to occur together in the same locations, while others are never observed coexisting. This question becomes particularly relevant for microorganisms thriving in the highly diluted waters of high mountain lakes, where biotic interactions might be required to make the most of an extreme environment. We studied a high-throughput gene data set of alpine lakes (>220 Pyrenean lakes) with cooccurrence network analysis to infer potential biotic interactions, using the combination of a probabilistic method for determining significant cooccurrences and coexclusions between pairs of species and a conceptual framework for classifying the nature of the observed cooccurrences and coexclusions. This computational approach (i) determined and quantified the importance of environmental variables and spatial distribution and (ii) defined potential interacting microbial assemblages. We determined the properties and relationships between these assemblages by examining node properties at the taxonomic level, indicating associations with their potential habitat sources (i.e., aquatic versus terrestrial) and their functional strategies (i.e., parasitic versus mixotrophic). Environmental variables explained fewer pairs in bacteria than in microbial eukaryotes for the alpine data set, with pH alone explaining the highest proportion of bacterial pairs. Nutrient composition was also relevant for explaining association pairs, particularly in microeukaryotes. We identified a reduced subset of pairs with the highest probability of species interactions (“interacting guilds”) that significantly reached higher occupancies and lower mean relative abundances in agreement with the carrying capacity hypothesis. The interacting bacterial guilds could be more related to habitat and microdispersal processes (i.e., aquatic versus soil microbes), whereas for microeukaryotes trophic roles (osmotrophs, mixotrophs, and parasitics) could potentially play a major role. Overall, our approach may add helpful information to guide further efforts for a mechanistic understanding of microbial interactions in situ. IMPORTANCE A fundamental question in biology is why some species tend to occur together in the same locations, while others are never observed to coexist. This question becomes particularly relevant for microorganisms thriving in the highly diluted waters of high mountain lakes, in which biotic interactions might be required to make the most of an extreme environment. Microbial metacommunities are too often only studied in terms of their environmental niches and geographic barriers since they show inherent difficulties to quantify biological interactions and their role as drivers of ecosystem functioning. Our study highlights that telling apart potential interactions from both environmental and geographic niches may help for the initial characterization of organisms with similar ecologies in a large scope of ecosystems, even when information about actual interactions is partial and limited. The multilayered statistical approach carried out here offers the possibility of going beyond taxonomy to understand microbiological behavior in situ.
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Zhang L, Gong X, Xu R, Guo K, Wang L, Zhou Y. Responses of mesophilic anaerobic sludge microbiota to thermophilic conditions: Implications for start-up and operation of thermophilic THP-AD systems. WATER RESEARCH 2022; 216:118332. [PMID: 35364350 DOI: 10.1016/j.watres.2022.118332] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 02/20/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Anaerobic digestion (AD) has been widely employed for wastewater and organic waste treatment, in which methanogenesis is highly driven by close microbial interactions among intricate microbial communities. However, the ecological processes underpinning the community assembly that support methanogenesis in such engineered ecosystems remain largely unknown, especially when exposed to challenging circumstances (e.g., high temperature, ammonium content). Here, eight AD bioreactors were seeded with four different inocula (two from full-scale mesophilic AD systems and the other two from lab-scale mesophilic AD systems), and were operated under thermophilic conditions (55 °C) for treating thermal hydrolysis process (THP) pre-treated waste activated sludge to investigate how mesophilic community responds to thermophilic conditions during the long-term cultivation. Results showed that the inocula collected from the full-scale systems were more resilient than that from the lab-scale systems, which may be primarily attributed to indigenous robust methanogens. As a result, the former efficiently generated methane which was predominantly contributed by Methanothermobacter and Methanosarcina (healthy AD ecosystem), while methanogenic activity was remarkably prohibited in the latter (dysfunctional AD ecosystem). Thermophilic environment was a strong selection force, resulting in the convergence of microbial communities in both the healthy and dysfunctional AD ecosystems. Deterministic processes predominated the community assembly regardless of AD ecosystem function, but stronger influences of stochastic processes were observed in dysfunctional AD ecosystems, which was likely attributable from the stronger effect of immigrants from the feedstock. As indicated by molecular ecological network analysis, the microbial network structures in the healthy AD ecosystems were more stable than those in the dysfunctional AD ecosystems. Although keystone taxa were different among the bioreactors, most of which played vital roles in organic hydrolysis/fermentation. To sum up, this study greatly improved our understanding of the relationships between microbiological traits and AD ecosystem function under thermophilic conditions, which could provide useful information to guide thermophilic AD (e.g., THP-AD) start-up and health diagnosis during operation.
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Affiliation(s)
- Liang Zhang
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Xianzhe Gong
- Institute of Marine Science and Technology, Shandong University, Qingdao, Shandong 266237, China
| | - Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Kun Guo
- School of Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Li Wang
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
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Wu JY, Hua ZL, Gu L. Per-, poly-fluoroalkyl substances (PFASs) and planktonic microbiomes: Identification of biotic and abiotic regulations in community coalescence and food webs. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 302:119078. [PMID: 35245616 DOI: 10.1016/j.envpol.2022.119078] [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: 11/08/2021] [Revised: 02/21/2022] [Accepted: 02/27/2022] [Indexed: 06/14/2023]
Abstract
The importance of per-, poly-fluoroalkyl substances (PFASs) effects on riverine microbiomes is receiving increased recognition in the environmental sciences. However, few studies have explored how PFASs affect microbiomes across trophic levels, specifically through predator-prey interactions. This study examined the community profiles of planktonic archaea, bacteria, fungi, algae, protozoa, and metazoa in a semi-industrial and agricultural river alongside their interactions with 15 detected PFASs. As abiotic factors, PFASs affected community coalescence more than biogenic substances (p < 0.05). For biotic regulations, sub-communities in rare biospheres (including always rare taxa-ART and critically rare taxa-CRT) contributed to spatial community coalescence more than sub-communities in abundant biospheres (always abundant taxa-AAT and critically abundant taxa-CAT) (p < 0.05). Metazoa-bacteria (Modularity = 1.971) and protozoa-fungi (1.723) were determined to be the most stable predator-prey networks. Based on pathway models, short-chain PFBA (C4) was shown to weaken the trophic transfer efficiencies from heterotrophic bacteria (HB) to heterotrophic flagellates (HF) (p < 0.05). Long-chain PFTeDA (C14) promoted HB to amoeba (p < 0.05), which we postulate is the pathway for PFTeDA to enter the microbial food chain. Our preliminary results elucidated the influence of PFASs on planktonic microbial food webs and highlighted the need to consider protecting and remediating riverine ecosystems containing PFASs.
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Affiliation(s)
- Jian-Yi Wu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Zu-Lin Hua
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China
| | - Li Gu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lake of Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, China; Yangtze Institute for Conservation and Development, Hohai University, Jiangsu, 210098, China.
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70
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Meng Y, Wang D, Wang P, Yu Z, Yuan S, Xia L, Meng F. The counteraction of anammox community to long-term nitrite stress: Crucial roles of rare subcommunity. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153062. [PMID: 35031357 DOI: 10.1016/j.scitotenv.2022.153062] [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: 11/02/2021] [Revised: 01/02/2022] [Accepted: 01/07/2022] [Indexed: 06/14/2023]
Abstract
Understanding the temporal dynamics and recovery of anammox community under nitrite stress is critical for successful application of anammox-related processes. Here, the response behaviors of anammox community were investigated to characterize the reactor performance and ecological function under varied levels of nitrite stress (changing from 0, 50, 100, 200 to 0 mg-N/L) across a large temporal scale (588 days). The nitrogen removal rates decreased from 0.51 ± 0.02 to 0.16 ± 0.04 kg-N/(m3·d) under nitrite stress from 0 to 200 mg-N/L, while it was recovered to 0.29 ± 0.06 kg-N/(m3·d) as nitrite stress terminated. A strong community succession was driven by the initial nitrite stress of 50 mg-N/L, while the community dissimilarity mainly resulted from the increased beta diversity of rare subcommunity. Meanwhile, the rare subcommunity with high functional redundancy likely warranted the functional resilience of anammox community across the nitrite stress gradients. Moreover, the increased positive interactions between anammox bacteria and side populations supported the resilience of anammox after discontinuing nitrite stress, which facilitated the recovery of nitrogen removal efficiency. This study deciphers the interspecies interactions and functional redundancy of rare subcommunity in shaping the robustness and resilience of anammox-related processes when treating nitrite fluctuated wastewater.
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Affiliation(s)
- Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Depeng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Pandeng Wang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhong Yu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Shasha Yuan
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Lichao Xia
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China
| | - Fangang Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology, Sun Yat-sen University, Guangzhou 510275, PR China; National Engineering Laboratory for Pollution Control and Waste Utilization in Livestock and Poultry Production, Changsha, Hunan 410125, PR China.
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71
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Li S, Fang J, Zhu X, Spencer RGM, Álvarez-Salgado XA, Deng Y, Huang T, Yang H, Huang C. Properties of sediment dissolved organic matter respond to eutrophication and interact with bacterial communities in a plateau lake. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 301:118996. [PMID: 35181452 DOI: 10.1016/j.envpol.2022.118996] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/19/2022] [Accepted: 02/12/2022] [Indexed: 06/14/2023]
Abstract
Sediment dissolved organic matter (DOM) in inland waters is commonly affected by environmental changes. However, knowledge about how sediment DOM responds to eutrophication and the associations between sediment DOM and bacterial communities requires further investigation. We selected a sediment core from Dianchi Lake (China) that was dated from 1864 to 2019 by the activity of radionuclides (210Pb and 137Cs). δ13CDOC changes fit well with the historical record that heavy eutrophic status in Dianchi Lake were observed since 1980s. Large amounts of dissolved organic carbon (DOC), chromophoric (CDOM) and fluorescent (FDOM) DOM accumulated at the top of the sediments during the eutrophication period (1982-present). The additional algae sources with a higher degradation rate altered the composition, aromaticity and humification of DOM. After long-term mineralization, the remaining DOM became more and more recalcitrant and kept a relatively stable level at older sediments. A co-occurrence network analysis revealed that Proteobacteria, Chloroflexi, Acidobacteriota, Bacteroidota and Desulfobacterota were the most abundant species at the phylum level and clustered into three primary modules. Different microbes shared unique preferences for niches, causing a heterogeneous bacterial distribution at different depths. We conducted Spearman's correlation and redundancy analysis (RDA) to explore potential interactions between bacterial community and sediment DOM. The richness and diversity of bacterial communities were positively related to DOM content, suggesting abundant DOM can produce more available resources for bacteria. RDA results showed some specific species might modify DOM composition and structure. This study suggests that sediment DOM properties were regulated by source transformation during eutrophication, and emphasizes the importance of microbial role on sediment biogeochemical process.
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Affiliation(s)
- Shuaidong Li
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China; Laboratorio de Geoquímica Orgánica, Instituto de Investigacións Mariñas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Jie Fang
- School of Geography and Ocean Science, Nanjing University, Nanjing 210023, PR China
| | - Xinshu Zhu
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Robert G M Spencer
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306, USA
| | - Xosé Antón Álvarez-Salgado
- Laboratorio de Geoquímica Orgánica, Instituto de Investigacións Mariñas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Yongcui Deng
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Tao Huang
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Hao Yang
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China
| | - Changchun Huang
- School of Geography, Nanjing Normal University, Nanjing 210023, PR China.
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72
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Zheng S, Zhou S, Lukwambe B, Nicholaus R, Yang W, Zheng Z. Bacterioplankton community assembly in migratory fish habitat: a case study of the southern East China Sea. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:33725-33736. [PMID: 35029823 DOI: 10.1007/s11356-022-18604-5] [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: 09/25/2021] [Accepted: 01/06/2022] [Indexed: 06/14/2023]
Abstract
The health conditions of fish habitats, which affect fish health, can be reflected by the structure and ecological function of the bacterioplankton community to some extent. However, studies on bacterioplankton in the whole habitat of migratory fish, which can be divided into different functional types, are still limited. To fill this gap, we investigated the characteristics of bacterioplankton communities in three habitat types in a typical migratory fish habitat, the southern East China Sea, using 16S rRNA gene amplicon sequencing. Our study showed that the structure of the bacterioplankton community was significantly divided according to habitat type. Dispersal limitation and heterogeneous selection both contributed to the bacterioplankton community assembly through estimation of β nearest taxon index (βNTI), and redundancy analysis (RDA) further explained that the water temperature, salinity, and nutrients were deterministic factors responsible for differences in the bacterioplankton community. Additionally, different ecological functional modules dominated by functional bacterioplankton in different habitat types were identified by co-occurrence network analysis, including a hydrocarbon-degrading module dominated by Psychrobacter and health-related modules containing Ascidiaceihabitans and Pseudoalteromonas. Based on the composition of environmental bacterioplankton, our findings provide a theoretical basis for understanding the distribution of different habitat types in the southern East China Sea during the breeding period of migratory fish.
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Affiliation(s)
- Shizhan Zheng
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
- Collaborative Innovation Center, Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China
| | - Shouheng Zhou
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China
| | - Betina Lukwambe
- School of Aquatic Sciences and Fisheries Technology, University of Dar Es Salaam, Dar es Salaam, Tanzania
| | - Regan Nicholaus
- Department of Natural Sciences, Mbeya University of Science and Technology, Mbeya, Tanzania
| | - Wen Yang
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
| | - Zhongming Zheng
- School of Marine Sciences, Ningbo University, Ningbo, 315211, China.
- Collaborative Innovation Center, Zhejiang Marine High-Efficiency and Healthy Aquaculture, Ningbo, China.
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73
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Pan C, Feng Q, Li Y, Li Y, Liu L, Yu X, Ren S. Rare soil bacteria are more responsive in desertification restoration than abundant bacteria. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:33323-33334. [PMID: 35025047 DOI: 10.1007/s11356-021-16830-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 09/27/2021] [Indexed: 06/14/2023]
Abstract
Soil microbes play key roles in ecosystem functions, especially in the recovery of ecosystems from disturbance, and exploring community assembly under changing environments has long been a central theme in microbial ecology. The response of abundant and rare bacteria in desertified land to restoration is still unclear. Here, we investigated the effects of vegetation restoration on the assemblage patterns of abundant and rare bacteria in soil across the four sandy lands (Hulunbeir, Horqin, Otindag, and Mu Us) in northern China. Our results revealed that abundant bacteria maintained a relatively stable state under restoration, whereas rare taxa were more responsive, indicating the higher resilience of the rare community to change. Our network analysis also showed that restoration promoted destabilizing properties in rare, but not in abundant, bacterial co-occurrence networks in soil. Environmental selection played a key role in abundant and rare community assembly under restoration. Of the two, the rare subcommunity was mainly affected by environmental filtering. The variations in the abundant and rare communities at the sampling sites under restoration were controlled mainly by plant species richness, and stronger effects were observed in the rare taxa. Overall, these results provide new insight into the mechanisms controlling bacterial community assembly in response to vegetation restoration.
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Affiliation(s)
- Chengchen Pan
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
- Qilian Mountains Eco-Environment Research Center, Lanzhou, 730000, Gansu, China
| | - Qi Feng
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China.
- Qilian Mountains Eco-Environment Research Center, Lanzhou, 730000, Gansu, China.
| | - Yulin Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
| | - Yuqiang Li
- Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou, 730000, Gansu, China
| | - Linde Liu
- College of Life Sciences, Ludong University, Yantai, 264025, Shandong, China.
| | - Xiaoya Yu
- School of Tourism and Resource Environment, Qiannan Normal University for Nationalities, Duyun, 558000, Guizhou, China
| | - Shilong Ren
- Environmental Research Institute, Shandong University, Qingdao, 266237, Shandong, China
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74
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Gautam A, Lear G, Lewis GD. Time after time: Detecting annual patterns in stream bacterial biofilm communities. Environ Microbiol 2022; 24:2502-2515. [PMID: 35466520 PMCID: PMC9324112 DOI: 10.1111/1462-2920.16017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/03/2022] [Accepted: 04/13/2022] [Indexed: 11/26/2022]
Abstract
To quantify the major environmental drivers of stream bacterial population dynamics, we modelled temporal differences in stream bacterial communities to quantify community shifts, including those relating to cyclical seasonal variation and more sporadic bloom events. We applied Illumina MiSeq 16S rRNA bacterial gene sequencing of 892 stream biofilm samples, collected monthly for 36‐months from six streams. The streams were located a maximum of 118 km apart and drained three different catchment types (forest, urban and rural land uses). We identified repeatable seasonal patterns among bacterial taxa, allowing their separation into three ecological groupings, those following linear, bloom/trough and repeated, seasonal trends. Various physicochemical parameters (light, water and air temperature, pH, dissolved oxygen, nutrients) were linked to temporal community changes. Our models indicate that bloom events and seasonal episodes modify biofilm bacterial populations, suggesting that distinct microbial taxa thrive during these events including non‐cyanobacterial community members. These models could aid in determining how temporal environmental changes affect community assembly and guide the selection of appropriate statistical models to capture future community responses to environmental change.
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Affiliation(s)
- Anju Gautam
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Gavin Lear
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
| | - Gillian D Lewis
- School of Biological Sciences, The University of Auckland, Auckland, 1010, New Zealand
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75
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Lu Z, Jing Z, Huang J, Ke Y, Li C, Zhao Z, Ao X, Sun W. Can we shape microbial communities to enhance biological activated carbon filter performance? WATER RESEARCH 2022; 212:118104. [PMID: 35114529 DOI: 10.1016/j.watres.2022.118104] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/16/2022] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
A new focus on biofiltration has emerged that aims to shape microbial communities to improve treatment efficacy. It is therefore necessary to understand the linkages between microbial community structure and biofilter function. However, the assembly and interaction of microbial communities in biological activated carbon (BAC) filters are unknown. In this study, we selected one coal-based granular activated carbon (GAC), GAC-13, with simultaneously developed micropore and micro-level macropore volume used for a bench-scale BAC column experiment, and compared it with other coal-based GACs and wood-based GAC in terms of the dissolved organic carbon (DOC) removal and microbial community characteristics. The results showed that there was no difference between the DOC removal efficiency of BAC-13 and the other two coal-based BAC filters with high iodine value in the period dominated by adsorption, while the DOC removal efficiency of BAC-13 (64.7±0.6%) was significantly higher than that of other BAC filters (36.3±0.8-54.1±0.4%) with a difference of 0.3-0.7 mg/L in DOC during the steady state. The bacterial communities were strongly assembled by deterministic rather than stochastic factors, where the surface polarity of GAC had a greater effect on the microbial communities than its physical properties. The corresponding co-occurrence network revealed that microbes in the BAC filter may be more cooperative than competitive. The keystone bacterium Hyphomicrobium, which had a relatively low abundance, contributed 0.3-1% more to the most abundant functions and produced 5-21 proteins/(g·GAC) more than the dominant bacterium Sphingobium. The metaproteomic-based approach could provide more accurate information regarding the contributions of different species to metabolic functions. The pore size distribution of GAC was found to be an important factor in determining BAC filter performance; the most important pore sizes were micropores and micro-level macropores (0.2-10 μm and >100 μm in diameter), and the latter impacted the abundance of keystone species. Overall, our findings provide new insights into shaping microbial communities by optimizing pore size structure to improve BAC performance, especially the abundance of keystone species.
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Affiliation(s)
- Zedong Lu
- School of Environment, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China
| | - Zibo Jing
- School of Environment, Tsinghua University, Beijing 100084, China; Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Jing Huang
- Beijing Drainage Group Co. Ltd. (BDG), Beijing 100022, China
| | - Yanchu Ke
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Chen Li
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Zhinan Zhao
- School of Environment, Tsinghua University, Beijing 100084, China; Beijing Engineering Research Center of Environmental Material for Water Purification, College of Chemical Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiuwei Ao
- School of Environment, Tsinghua University, Beijing 100084, China
| | - Wenjun Sun
- School of Environment, Tsinghua University, Beijing 100084, China; Research Institute for Environmental Innovation (Suzhou) Tsinghua, Suzhou 215163, China.
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76
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Del Rio-Hortega L, Martín-Forés I, Castro I, De Miguel JM, Acosta-Gallo B. Network-based analysis reveals differences in plant assembly between the native and the invaded ranges. NEOBIOTA 2022. [DOI: 10.3897/neobiota.72.72066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Associated with the introduction of alien species in a new area, interactions with other native species within the recipient community occur, reshaping the original community and resulting in a unique assemblage. Yet, the differences in community assemblage between native and invaded ranges remain unclear. Mediterranean grasslands provide an excellent scenario to study community assembly following transcontinental naturalisation of plant species. Here, we compared the community resemblance of plant communities in Mediterranean grasslands from both the native (Spain) and invaded (Chile) ranges. We used a novel approach, based on network analysis applied to co-occurrence analysis in plant communities, allowing us to study the co-existence of native and alien species in central Chile. This useful methodology is presented as a step forward in invasion ecology studies and conservation strategies. We found that community structure differed between the native and the invaded range, with alien species displaying a higher number of connections and, therefore, acting as keystones to sustain the structure within the invaded community. Alien species acting like keystones within the Chilean grassland communities might exacerbate the threat posed by biological invasions for the native biodiversity assets. Controlling the spread of the alien species identified here as keystones should help managing potential invasion in surrounding areas. Network analyses is a free, easy-to-implement and straightforward visual tool that can be widely used to reveal shifts in native communities and elucidate the role of multiple invaders into communities.
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77
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Wang D, Huang K, He X, Zhang XX, Meng Y. Varied interspecies interactions between anammox and denitrifying bacteria enhanced nitrogen removal in a single-stage simultaneous anammox and denitrification system. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152519. [PMID: 34968587 DOI: 10.1016/j.scitotenv.2021.152519] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 12/08/2021] [Accepted: 12/14/2021] [Indexed: 05/05/2023]
Abstract
The simultaneous anammox and denitrification (SAD) system has received growing interest for the enhanced nitrogen removal, while the ecological traits of microbial community including spatial distribution characteristics, assembly processes and interspecies interactions have not been fully unraveled. The present study applied metagenomics and ecological analysis methods to gain the ecological traits of microbial communities in the SAD system across different organic substrate loadings. Results showed that organic matter significantly affected the bioreactor performance, and the optimal total nitrogen removal efficiency reached 93.4 ± 0.7% under the COD concentrations of 180 ± 18.2 mg/L. Functional organisms including Candidatus Brocadia (3.9%), Denitratisoma (1.6%), Dokdonella (4.4%) and Thauera (4.6%) obviously enriched under the optimal organic loading conditions. Moreover, microbial communities were significantly governed by deterministic process under high organic concentrations, and the denitrifying organisms displayed important ecological roles in the communities. Although anammox bacteria obviously enriched at the middle of bioreactor, it possessed the highest expression activities at both bottom and middle sites. Denitrifying bacteria that enriched at the bottom sites strongly achieved nitrate reduction and provided nitrite for anammox bacteria, while these organisms trended to compete nitrite with anammox bacteria at the middle site. These findings highlight the importance of microbial ecology in the SAD systems, which may expand our understanding of the synergistic patterns between anammox and denitrifying bacteria.
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Affiliation(s)
- Depeng Wang
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China; State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Kailong Huang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China; Nanjing Jiangdao Institute of Environmental Research Co., Ltd., Nanjing 210019, China
| | - Xiwei He
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Xu-Xiang Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, School of the Environment, Nanjing University, Nanjing 210023, China
| | - Yabing Meng
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou 510275, China.
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78
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Dong K, Yu Z, Kerfahi D, Lee SS, Li N, Yang T, Adams JM. Soil microbial co-occurrence networks become less connected with soil development in a high Arctic glacier foreland succession. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152565. [PMID: 34953844 DOI: 10.1016/j.scitotenv.2021.152565] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Revised: 11/30/2021] [Accepted: 12/16/2021] [Indexed: 06/14/2023]
Abstract
Classically, ecologists have considered that biota becomes more integrated and interdependent with ecosystem development in primary successional environments. However, recent work on soil microbial communities suggests that there may in fact be no change in network integration over successional time series. Here, we performed a test of this principle by identifying network-level topological features of the soil microbial co-occurrence networks in the primary successional foreland environment of the retreating high-Arctic glacier of Midtre Lovénbreen, Svalbard. Soil was sampled at sites along the foreland of inferred ages 10-90 years since deglaciation. DNA was extracted and amplicon sequenced for 16 s rRNA genes for bacteria and ITS1 region for fungi. Despite the chronologically-related soil pH decline and organic C/N accumulation, analysis on network-level topological features showed network integration did not change with inferred chronological ages, whereas network integration declined with decreasing pH and increasing total organic carbon (TOC) - both factors that can be viewed as an indicator of soil development. We also found that bacteria played a greater role in the network structure than fungi, with all keystone species in the microbial co-occurrence network being bacteria species. Both number and relative abundance of the keystone species were significantly higher when soil pH increased or TOC decreased. It appears that in the more extreme and less productive conditions of early primary succession, integration between members of soil biota into consortia may play a greater role in niche adaptation and survival. Our finding also emphasizes that ecosystem development is not simply a product of time but is influenced by locally heterogeneous factors.
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Affiliation(s)
- Ke Dong
- Life Science Major, Kyonggi University, Suwon, South Korea
| | - Zhi Yu
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, South Korea
| | - Sang-Seob Lee
- College of Biotechnology and Bioengineering, Sungkyunkwan University, Suwon, South Korea
| | - Nan Li
- Key laboratory of Ministry of Education for Environment Change and Resources Use in Beibu Gulf, Nanning Normal University, Nanning, China
| | - Teng Yang
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jonathan M Adams
- School of Geographic and Oceanographic Sciences, Nanjing University, Nanjing, China.
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79
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Krasnopeev AY, Bukin YS, Potapov SA, Belykh OI. Data Filtering Algorithm for DNA Metabarcoding Studies of Ecological Communities. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422020089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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80
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Qian X, Lü Q, He X, Wang Y, Li H, Xiao Q, Zheng X, Lin R. Pseudomonas sp. TCd-1 significantly alters the rhizosphere bacterial community of rice in Cd contaminated paddy field. CHEMOSPHERE 2022; 290:133257. [PMID: 34906525 DOI: 10.1016/j.chemosphere.2021.133257] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/06/2021] [Accepted: 12/09/2021] [Indexed: 06/14/2023]
Abstract
Cadmium (Cd) pollution of paddy soils is one of the main concerns causing food security and environmental problems. Microbial bioremediation is an effective and eco-friendly measure that uses microbes to reduce Cd accumulation in crops. Additionally, rhizosphere bacterial communities also act essential roles in crop tolerance of heavy metals. However, the effects of inoculations with Cd resistant bacteria on crop rhizosphere bacterial communities under Cd exposure are largely unknown. In this study, we used high-throughput 16S rRNA gene sequencing technologies to explore the community structure and co-occurrence network of the rhizosphere bacterial communities associated with the rice crop under different Cd treatments and the application of Cd-tolerant strain Pseudomonas sp. TCd-1. We found that the strain TCd-1 both significantly reduced the rhizobacterial alpha diversity and changed the beta diversity. PERMANOVA and NMDS analysis showed that Cd stress and TCd-1 strain could act as strong environmental filters resulting in observable differentiation of rhizobacterial community composition among different groups. In addition, RDA results indicated that the rhizosphere pH, root Cd content, catalase (CAT), urease (URE), gibberellic acid (GA3) exert significant association with rhizosphere bacterial assembly. PICRUSt analysis revealed that the TCd-1 strain improved the metabolic capacity of rhizosphere bacteria under Cd stress. Furthermore, co-occurrence network topological features and keystone taxa also varied among different groups. This study could provide necessary insights into developing an efficient bioremediation and safe production of rice crops in Cd contaminated paddy fields with the application of Pseudomonas sp. TCd-1 strain, as well as advance our understanding of the principles of rhizosphere bacterial community assembly under Cd stress.
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Affiliation(s)
- Xin Qian
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Qixin Lü
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaosan He
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yujie Wang
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hanzhou Li
- Biomarker Technologies Corporation, Beijing, 101300, China
| | - Qingtie Xiao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xinyu Zheng
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ruiyu Lin
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Fujian Provincial Key Laboratory of Agroecological Processing and Safety Monitoring, School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Key Laboratory of Crop Ecology and Molecular Physiology of Fujian Province, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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81
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Prevalence of Actinobacteria in the production of 2-methylisoborneol and geosmin, over Cyanobacteria in a temperate eutrophic reservoir. CHEMICAL ENGINEERING JOURNAL ADVANCES 2022. [DOI: 10.1016/j.ceja.2021.100226] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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82
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Different Assembly Patterns of Planktonic and Sedimentary Bacterial Community in a Few Connected Eutrophic Lakes. WATER 2022. [DOI: 10.3390/w14050723] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The mechanism of bacterial community assembly has been the hot spot in the field of microbial ecology and it is difficult to quantitatively estimate the influences of different ecological processes. Here, a total of 23 pairs of planktonic and sedimentary samples were collected from five lakes in Wuhan, China. significant higher α-diversity (p < 0.001) and β-diversity (p < 0.001) of bacterial communities were observed in sediment than those in water. Some phylum had linear relationships with the comprehensive TSI (TSIc) by regression analysis. Non-metric multidimensional scaling (NMDS) and redundancy analysis (RDA) revealed that the depth of water, NO3−-N, NH4+-N, PO43−, and CODcr were the key environmental variables in planktonic bacterial communities, whereas in sediment they were the depth, NO3−-N, and NH4+-N. Furthermore, variation partitioning analysis (VPA) showed that spatial and environmental factors could only explain 40.2% and 27.9% of the variation in planktonic and sedimentary bacterial communities, respectively. More importantly, null model analysis suggested that different assembly mechanisms were found between in water and in sediment with the fact that planktonic bacterial community assembly was mainly driven by dispersal limitation process whereas variable selection process played a vital role in that of sediment.
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83
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Kodera SM, Das P, Gilbert JA, Lutz HL. Conceptual strategies for characterizing interactions in microbial communities. iScience 2022; 25:103775. [PMID: 35146390 PMCID: PMC8819398 DOI: 10.1016/j.isci.2022.103775] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Understanding the sets of inter- and intraspecies interactions in microbial communities is a fundamental goal of microbial ecology. However, the study and quantification of microbial interactions pose several challenges owing to their complexity, dynamic nature, and the sheer number of unique interactions within a typical community. To overcome such challenges, microbial ecologists must rely on various approaches to distill the system of study to a functional and conceptualizable level, allowing for a practical understanding of microbial interactions in both simplified and complex systems. This review broadly addresses the role of several conceptual approaches available for the microbial ecologist’s arsenal, examines specific tools used to accomplish such approaches, and describes how the assumptions, expectations, and philosophies underlying these tools change across scales of complexity.
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Affiliation(s)
- Sho M Kodera
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA
| | - Promi Das
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Jack A Gilbert
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA 92037, USA.,Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA
| | - Holly L Lutz
- Center for Microbiome Innovation, University of California San Diego, La Jolla, CA 92093, USA.,Department of Pediatrics, University of California San Diego, La Jolla, CA 92161, USA.,Negaunee Integrative Collections Center, Field Museum of Natural History, Chicago, IL 60605, USA
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84
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Li H, Luo L, Tang B, Guo H, Cao Z, Zeng Q, Chen S, Chen Z. Dynamic changes of rhizosphere soil bacterial community and nutrients in cadmium polluted soils with soybean-corn intercropping. BMC Microbiol 2022; 22:57. [PMID: 35168566 PMCID: PMC8845239 DOI: 10.1186/s12866-022-02468-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Soybean-corn intercropping is widely practised by farmers in Southwest China. Although rhizosphere microorganisms are important in nutrient cycling processes, the differences in rhizosphere microbial communities between intercropped soybean and corn and their monoculture are poorly known. Additionally, the effects of cadmium (Cd) pollution on these differences have not been examined. Therefore, a field experiment was conducted in Cd-polluted soil to determine the effects of monocultures and soybean-corn intercropping systems on Cd concentrations in plants, on rhizosphere bacterial communities, soil nutrients and Cd availability. Plants and soils were examined five times in the growing season, and Illumina sequencing of 16S rRNA genes was used to analyze the rhizosphere bacterial communities. RESULTS Intercropping did not alter Cd concentrations in corn and soybean, but changed soil available Cd (ACd) concentrations and caused different effects in the rhizosphere soils of the two crop species. However, there was little difference in bacterial community diversity for the same crop species under the two planting modes. Proteobacteria, Chloroflexi, Acidobacteria, Actinobacteria and Firmicutes were the dominant phyla in the soybean and corn rhizospheres. In ecological networks of bacterial communities, intercropping soybean (IS) had more module hubs and connectors, whereas intercropped corn (IC) had fewer module hubs and connectors than those of corresponding monoculture crops. Soil organic matter (SOM) was the key factor affecting soybean rhizosphere bacterial communities, whereas available nutrients (N, P, K) were the key factors affecting those in corn rhizosphere. During the cropping season, the concentration of soil available phosphorus (AP) in the intercropped soybean-corn was significantly higher than that in corresponding monocultures. In addition, the soil available potassium (AK) concentration was higher in intercropped soybean than that in monocropped soybean. CONCLUSIONS Intercropped soybean-corn lead to an increase in the AP concentration during the growing season, and although crop absorption of Cd was not affected in the Cd-contaminated soil, soil ACd concentration was affected. Intercropped soybean-corn also affected the soil physicochemical properties and rhizosphere bacterial community structure. Thus, intercropped soybean-corn was a key factor in determining changes in microbial community composition and networks. These results provide a basic ecological framework for soil microbial function in Cd-contaminated soil.
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Affiliation(s)
- Han Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Luyun Luo
- Yangtze Normal University, Chongqing, China.
| | - Bin Tang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Huanle Guo
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China.
| | - Zhongyang Cao
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Qiang Zeng
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Songlin Chen
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Zhihui Chen
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China.
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85
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Abstract
Microbial composition and functions in the rhizosphere—an important microbial hotspot—are among the most fascinating yet elusive topics in microbial ecology. We used 557 pairs of published 16S rDNA amplicon sequences from the bulk soils and rhizosphere in different ecosystems around the world to generalize bacterial characteristics with respect to community diversity, composition, and functions. The rhizosphere selects microorganisms from bulk soil to function as a seed bank, reducing microbial diversity. The rhizosphere is enriched in Bacteroidetes, Proteobacteria, and other copiotrophs. Highly modular but unstable bacterial networks in the rhizosphere (common for r-strategists) reflect the interactions and adaptations of microorganisms to dynamic conditions. Dormancy strategies in the rhizosphere are dominated by toxin–antitoxin systems, while sporulation is common in bulk soils. Functional predictions showed that genes involved in organic compound conversion, nitrogen fixation, and denitrification were strongly enriched in the rhizosphere (11–182%), while genes involved in nitrification were strongly depleted. Understanding soil microbiota dynamics is key the development of soil-based sustainable agriculture and conservation strategies. This meta-analysis shows that bulk soil functions as a seed bank for the rhizosphere, which encompasses a rich microbiota adapted to dynamic conditions in hotpots.
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86
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Li N, Li X, Fan XY. Storage tank as a pretreatment unit for rainwater cleaner production: Role of biofilm bacterial communities and functional genera in water quality improvement. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 303:114118. [PMID: 34838388 DOI: 10.1016/j.jenvman.2021.114118] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 10/30/2021] [Accepted: 11/13/2021] [Indexed: 06/13/2023]
Abstract
This study investigated the water purification function and mechanism of biofilm in storage tank, with a view to using it as a pretreatment unit for rainwater cleaner production. Shortening the hydraulic retention time (HRT) of storage tank from 12 to 4 h improved the pollutants removal performance and reduced the suspended bacteria counts. The accumulation of abundant taxa and succession of rare taxa were observed with biofilm development. Positive correlations within and across different bacterial taxa were dominant in the network, and some rare genera (Ralstonia and Micropruina) were identified as hub bacteria. Candidatus Nitrospira nitrosa and Nitrospira sp. ENR4 were two identified complete ammonia oxidizers. Denitrifying bacteria tended to enrich and formed more complex interactions over time. The main nitrogen metabolism pathways may be ammonia assimilatory, complete denitrification and dissimilatory/assimilatory nitrate reduction. HRT was negatively correlated with most dominant genera, and contributed 20.35% to the variation of functional taxa. This study highlights the self-purification function and micro-ecology of storage tank, and provides a new insight for its role in rainwater cleaner production process.
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Affiliation(s)
- Na Li
- Faculty of Architecture, Civil and Transportation Engineering, Beijing University of Technology, Beijing, 100124, PR China
| | - Xing Li
- Faculty of Architecture, Civil and Transportation Engineering, Beijing University of Technology, Beijing, 100124, PR China.
| | - Xiao-Yan Fan
- Faculty of Architecture, Civil and Transportation Engineering, Beijing University of Technology, Beijing, 100124, PR China
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87
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Zhang L, Guo K, Wang L, Xu R, Lu D, Zhou Y. Effect of sludge retention time on microbial succession and assembly in thermal hydrolysis pretreated sludge digesters: Deterministic versus stochastic processes. WATER RESEARCH 2022; 209:117900. [PMID: 34902758 DOI: 10.1016/j.watres.2021.117900] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 11/06/2021] [Accepted: 11/24/2021] [Indexed: 06/14/2023]
Abstract
Thermal hydrolysis process (THP) assisted anaerobic digestion (AD) has been demonstrated to be an efficient approach to improve biogas production and solids reduction. Given the faster reaction kinetics in the THP-AD system, reduction of sludge retention time (SRT) is possible. However, a comprehensive understanding of the effects of sludge retention time (SRT) on microbial dynamics and community assemblages is still lacking in THP-AD systems. Thus, twelve THP-AD reactors were operated at different SRTs (10-30 d) to fulfill the knowledge gap. Results showed that, although all the bioreactors displayed good performance, shorter SRT reactors (SRT 10 d) took a longer time to reach the stable state. The total biogas production at SRT of 10 d was lower than that at other longer SRTs, attributing to the limited hydrolytic/fermentative capacities of AD microbiomes. Different SRTs resulted in distinct succession patterns of AD microbiomes. THP sludge reduced the microbial diversity in all the bioreactors over time, but longer SRTs maintained higher biodiversity. Null model analysis suggested that THP-AD microbial community assembly was predominately driven by deterministic selection at the tested SRT range, but stochasticity increased with elevated SRTs, likely attributing to the immigrants from the feedstock. Phylogenetic molecular ecological networks (pMENs) analysis revealed more stable network structures at longer SRTs, evidenced by the lower modularity, shorter harmonic geodesic distance, and higher connectivity. The potential keystone taxa under varied SRTs were identified, some of which were hydrolytic/fermentative bacteria (e.g., Peptostreptococcus, Lutispora, Synergistaceae), suggesting that these species related to organic hydrolysis/fermentation even with low-abundance could still play pivotal ecological roles in maintaining the THP-AD microbial community structure and functions. Collectively, this study provides comprehensive and in-depth insights into the mechanisms underlying community assembly in THP-AD reactors, which could aid in diagnosing system stability.
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Affiliation(s)
- Liang Zhang
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Kun Guo
- Ecological and Environmental Sciences, East China Normal University, Shanghai, China
| | - Li Wang
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Ronghua Xu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, China
| | - Dan Lu
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Yan Zhou
- Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore; School of Civil and Environmental Engineering, Nanyang Technological University, Singapore 639798, Singapore.
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88
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Understanding Interaction Patterns within Deep-Sea Microbial Communities and Their Potential Applications. Mar Drugs 2022; 20:md20020108. [PMID: 35200637 PMCID: PMC8874374 DOI: 10.3390/md20020108] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 01/17/2022] [Accepted: 01/21/2022] [Indexed: 11/17/2022] Open
Abstract
Environmental microbes living in communities engage in complex interspecies interactions that are challenging to decipher. Nevertheless, the interactions provide the basis for shaping community structure and functioning, which is crucial for ecosystem service. In addition, microbial interactions facilitate specific adaptation and ecological evolution processes particularly essential for microbial communities dwelling in resource-limiting habitats, such as the deep oceans. Recent technological and knowledge advancements provide an opportunity for the study of interactions within complex microbial communities, such as those inhabiting deep-sea waters and sediments. The microbial interaction studies provide insights into developing new strategies for biotechnical applications. For example, cooperative microbial interactions drive the degradation of complex organic matter such as chitins and celluloses. Such microbiologically-driven biogeochemical processes stimulate creative designs in many applied sciences. Understanding the interaction processes and mechanisms provides the basis for the development of synthetic communities and consequently the achievement of specific community functions. Microbial community engineering has many application potentials, including the production of novel antibiotics, biofuels, and other valuable chemicals and biomaterials. It can also be developed into biotechniques for waste processing and environmental contaminant bioremediation. This review summarizes our current understanding of the microbial interaction mechanisms and emerging techniques for inferring interactions in deep-sea microbial communities, aiding in future biotechnological and therapeutic applications.
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89
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Kumar D, Downs LP, Adegoke A, Machtinger E, Oggenfuss K, Ostfeld RS, Embers M, Karim S. An Exploratory Study on the Microbiome of Northern and Southern Populations of Ixodes scapularis Ticks Predicts Changes and Unique Bacterial Interactions. Pathogens 2022; 11:130. [PMID: 35215074 PMCID: PMC8880235 DOI: 10.3390/pathogens11020130] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/13/2022] [Accepted: 01/19/2022] [Indexed: 02/04/2023] Open
Abstract
The black-legged tick (Ixodes scapularis) is the primary vector of Borrelia burgdorferi, the causative agent of Lyme disease in North America. However, the prevalence of Lyme borreliosis is clustered around the Northern States of the United States of America. This study utilized a metagenomic sequencing approach to compare the microbial communities residing within Ix. scapularis populations from northern and southern geographic locations in the USA. Using a SparCC network construction model, we performed potential interactions between members of the microbial communities from Borrelia burgdorferi-infected tissues of unfed and blood-fed ticks. A significant difference in bacterial composition and diversity was found between northern and southern tick populations. The network analysis predicted a potential antagonistic interaction between endosymbiont Rickettsia buchneri and Borrelia burgdorferi sensu lato. The network analysis, as expected, predicted significant positive and negative microbial interactions in ticks from these geographic regions, with the genus Rickettsia, Francisella, and Borreliella playing an essential role in the identified clusters. Interactions between Rickettsia buchneri and Borrelia burgdorferi sensu lato need more validation and understanding. Understanding the interplay between the microbiome and tick-borne pathogens within tick vectors may pave the way for new strategies to prevent tick-borne infections.
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Affiliation(s)
- Deepak Kumar
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (L.P.D.); (A.A.)
| | - Latoyia P. Downs
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (L.P.D.); (A.A.)
| | - Abdulsalam Adegoke
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (L.P.D.); (A.A.)
| | - Erika Machtinger
- Department of Entomology, Pennsylvania State University, University Park, PA 16802, USA;
| | - Kelly Oggenfuss
- Cary Institute of Ecosystem Studies, Millbrook, NY 12542, USA; (K.O.); (R.S.O.)
| | - Richard S. Ostfeld
- Cary Institute of Ecosystem Studies, Millbrook, NY 12542, USA; (K.O.); (R.S.O.)
| | - Monica Embers
- Division of Immunology, Tulane National Primate Research Center, 18703 Three Rivers Rd., Covington, LA 70433, USA;
| | - Shahid Karim
- School of Biological, Environmental and Earth Sciences, The University of Southern Mississippi, Hattiesburg, MS 39406, USA; (D.K.); (L.P.D.); (A.A.)
- Center for Molecular and Cellular Biosciences, University of Southern Mississippi, Hattiesburg, MS 39406, USA
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90
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Xia F, Hu S, Zheng X, Wang MW, Zhang CC, Wu ZN, Sun YJ. New insights into metabolomics profile generation in fermented tea: the relevance of bacteria and metabolites in Fuzhuan brick tea. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:350-359. [PMID: 34143449 DOI: 10.1002/jsfa.11365] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/16/2021] [Accepted: 06/18/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND The contribution of bacteria to fermented tea is not clear and the associated research is relatively limited. To reveal the role of microorganisms in fermented tea processing, the microbial community and metabolites of Fuzhuan brick tea (FBT), a Chinese traditional fermented tea, were revealed via high-throughput sequencing and liquid chromatography-mass spectrometry (LC-MS). RESULTS In FBT, bacterial communities had a higher abundance and diversity, Lactococcus and Bacillus were the main bacteria, and Eurotium was the predominant fungus. The predictive metabolic function indicated the pathways of cellular growth, environmental information, genetics and material metabolism of bacterial communities were abundant, whereas the fungal community predictive metabolic function was almost saprotroph. Using LC-MS, 1143 and 536 metabolites were defined in positive and negative ion mode, respectively. There were essential correlations between bacterial populations and metabolites, such that Bacillus was correlated significantly with 44 metabolites (P < 0.05) and Enterococcus was significantly associated with 15 metabolites (P < 0.05). Some of the main active components were significantly correlated with the bacteria, such as Enterococcus, Lactococcus and Carnobacterium. CONCLUSION Not only Eurotium, but also the bacteria were involved in the changes of metabolomics profile in fermented FBT. The present study assists in providing new insights into metabolomics profile generation in fermented tea. The present research lays a foundation for controlling the FBT fermentation by artificial inoculation to improve quality. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Fei Xia
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Song Hu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Xue Zheng
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Meng-Wen Wang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Chu-Chu Zhang
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Zi-Ning Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
| | - Yu-Jiao Sun
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, China
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91
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Soil Bacterial Community Shifts Are Driven by Soil Nutrient Availability along a Teak Plantation Chronosequence in Tropical Forests in China. BIOLOGY 2021; 10:biology10121329. [PMID: 34943244 PMCID: PMC8698287 DOI: 10.3390/biology10121329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/03/2021] [Accepted: 12/10/2021] [Indexed: 12/24/2022]
Abstract
Simple Summary Tropical forests play an important role in the global carbon cycle, especially in the context of global climate change. Soil microorganisms are essential to the functions, services, and productivity of terrestrial ecosystems as a link to maintain the connections and interactions between the aboveground and belowground ecosystems. The interactions between plants and the soil microbiome are crucial for plant growth, health, and resistance to stressors. However, information on the response of soil microbial communities to a chronosequence of woody plants is lacking, especially in tropical forests. This study compares the soil properties, diversity, composition, and co-occurrence patterns of bacterial communities in the rhizosphere and bulk soils along a teak plantation chronosequence. The results show that the composition and co-occurrence patterns of the bacterial communities are statistically different among the plantations, while stand age has no significant impact on soil bacterial alpha diversity. The results further show that soil nutrients play a key role in shaping the soil bacterial community. The study also provides information about the dynamics and characteristics of these soil bacterial communities and adds valuable information that may underpin new strategies for the management of teak plantations. Abstract Soil bacterial communities play crucial roles in ecosystem functions and biogeochemical cycles of fundamental elements and are sensitive to environmental changes. However, the response of soil bacterial communities to chronosequence in tropical ecosystems is still poorly understood. This study characterized the structures and co-occurrence patterns of soil bacterial communities in rhizosphere and bulk soils along a chronosequence of teak plantations and adjacent native grassland as control. Stand ages significantly shifted the structure of soil bacterial communities but had no significant impact on bacterial community diversity. Bacterial community diversity in bulk soils was significantly higher than that in rhizosphere soils. The number of nodes and edges in the bacterial co-occurrence network first increased and then decreased with the chronosequence. The number of strongly positive correlations per network was much higher than negative correlations. Available potassium, total potassium, and available phosphorus were significant factors influencing the structure of the bacterial community in bulk soils. In contrast, urease, total potassium, pH, and total phosphorus were significant factors affecting the structure of the bacterial community in the rhizosphere soils. These results indicate that available nutrients in the soil are the main drivers regulating soil bacterial community variation along a teak plantation chronosequence.
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Yang Y, Shi Y, Kerfahi D, Ogwu MC, Wang J, Dong K, Takahashi K, Moroenyane I, Adams JM. Elevation-related climate trends dominate fungal co-occurrence network structure and the abundance of keystone taxa on Mt. Norikura, Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 799:149368. [PMID: 34352461 DOI: 10.1016/j.scitotenv.2021.149368] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/15/2021] [Accepted: 07/25/2021] [Indexed: 06/13/2023]
Abstract
Soil fungi play an important role in promoting nutrient cycling and maintaining ecosystem stability. Yet, there has been little understanding of how fungal co-occurrence networks differ along elevational climate gradients, a topic of interest to both macroecology and climate change studies. Based on high-throughput sequencing technology, we investigated the trend in co-occurrence network structure of soil fungal communities at 11 elevation levels along a 2300 m elevation gradient on Mt. Norikura, Japan, and identified the keystone taxa in the network, hypothesizing a progressive decline in network connectivity with elevation due to decreased plant diversity and enhanced environmental stress caused by changes in climate and soil characteristics. Our results demonstrated that network-level topological features such as network size, average degree, clustering coefficient, and modularity decreased significantly with increasing elevation, indicating that the fungal OTUs at low elevation were more closely associated and the network structure was more compact at low elevations. This conclusion was verified by the negative correlation between positive cohesion, negative cohesion and elevation. Moreover, the negative/positive cohesion ratio reached its peak value in mid-elevations with moderate environmental stress, indicating that the fungal community structure in mid-elevations was more stable than that at other elevations. We also found that the keystone taxa were more abundant at lower elevations. Furthermore, statistical analysis revealed that against a background of uniform geology, climate may play a dominant role in determining the properties and intensity of soil fungal networks, and significantly affect the abundance distribution of keystone taxa. These findings enhance understanding of the pattern and mechanism of the fungal community co-occurrence network along elevation, as well as the responses of microorganisms to climate change on a vertical scale in montane ecosystems. IMPORTANCE: Exploration of the elevational distribution of microbial networks and their driving factors and mechanisms may provide opportunities for predicting potential impacts of environmental changes, on ecosystem functions and biogeographic patterns at a broad scale. Although many studies have explored patterns of fungal community diversity and composition along various environmental gradients, it is unclear how the topological structure of co-occurrence networks shifts along elevational temperature gradients. In this study, we found that the connectivity of the fungal community decreased with increasing elevation and that climate was the dominant factor regulating co-occurrence patterns, apparently acting indirectly through soil characteristics. Our results also suggest that higher elevations on mountains have fewer keystone taxa than low elevations. These patterns may be related to the decrease of plant diversity and the increase of environmental stress along elevation gradients.
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Affiliation(s)
- Ying Yang
- School of Geography and Oceanography, Nanjing University, Nanjing, China
| | - Yu Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Henan, China
| | - Dorsaf Kerfahi
- School of Natural Sciences, Department of Biological Sciences, Keimyung University, Daegu, Republic of Korea
| | - Matthew C Ogwu
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Marche - Floristic Research Center of the Apennines, Gran Sasso and Monti della Laga National Park, San Colombo, Barisciano, L'Aquila, Italy
| | - Jianjun Wang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ke Dong
- Life Science Major, Kyonggi University, Suwon, South Korea
| | - Koichi Takahashi
- Department of Biological Sciences, Shinsu University, Matsumoto, Japan
| | - Itumeleng Moroenyane
- Institut National Recherche Scientifique Centre, Institut Armand Frappier Santé Biotechnologie, Quebéc, Canada
| | - Jonathan M Adams
- School of Geography and Oceanography, Nanjing University, Nanjing, China.
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93
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Han F, Li X, Zhang M, Liu Z, Han Y, Li Q, Zhou W. Solid-phase denitrification in high salinity and low-temperature wastewater treatment. BIORESOURCE TECHNOLOGY 2021; 341:125801. [PMID: 34438282 DOI: 10.1016/j.biortech.2021.125801] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 08/12/2021] [Accepted: 08/14/2021] [Indexed: 06/13/2023]
Abstract
Nitrogen removal from wastewater is often deteriorated under high salinity and low temperature. Solid-phase denitrification (SPD) might improve total nitrogen removal efficiency (TNRE) by stably supplying carbon resources under adverse conditions. In this study, an SPD biofilm reactor was successfully established by inoculating halophilic sludge and filling poly (butanediol succinate) (PBS) granules, and achieved over 96% TNRE at low temperature. More extracellular polysaccharides were produced at low temperature. Microbial network analysis evidenced dominant heterotrophic denitrifiers (Marinicella, Fusibacter, Saccharicrinis and Vitellibacter) at 25 °C were replaced by genera Melioribacter, Marinobacter, Desulfatitalea and Thiomicrospira at 15 °C. At low temperature, genes nirS and narG might be mainly responsible for denitrification. Fluorescence spectrum coupled with fluorescence regional integration and parallel factor analysis revealed low temperature increased the proportion of proteins of soluble microbial products. This study provides guidance for the practical application of SPD in the treatment of high salinity and low-temperature wastewater.
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Affiliation(s)
- Fei Han
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266000, China
| | - Xuan Li
- Shandong Academy for Environmental Planning, Jinan, Shandong 250002, China
| | - Mengru Zhang
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266000, China
| | - Zhe Liu
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266000, China
| | - Yufei Han
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266000, China
| | - Qian Li
- School of Environmental Science and Engineering, Shandong University, Qingdao, Shandong 266000, China
| | - Weizhi Zhou
- School of Civil Engineering, Shandong University, Jinan, Shandong 250002, China.
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94
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Wang H, Chen F, Zhang C, Wang M, Kan J. Estuarine gradients dictate spatiotemporal variations of microbiome networks in the Chesapeake Bay. ENVIRONMENTAL MICROBIOME 2021; 16:22. [PMID: 34838139 PMCID: PMC8627074 DOI: 10.1186/s40793-021-00392-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 11/10/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND Annually reoccurring microbial populations with strong spatial and temporal variations have been identified in estuarine environments, especially in those with long residence time such as the Chesapeake Bay (CB). However, it is unclear how microbial taxa cooccurr and how the inter-taxa networks respond to the strong environmental gradients in the estuaries. RESULTS Here, we constructed co-occurrence networks on prokaryotic microbial communities in the CB, which included seasonal samples from seven spatial stations along the salinity gradients for three consecutive years. Our results showed that spatiotemporal variations of planktonic microbiomes promoted differentiations of the characteristics and stability of prokaryotic microbial networks in the CB estuary. Prokaryotic microbial networks exhibited a clear seasonal pattern where microbes were more closely connected during warm season compared to the associations during cold season. In addition, microbial networks were more stable in the lower Bay (ocean side) than those in the upper Bay (freshwater side). Multivariate regression tree (MRT) analysis and piecewise structural equation modeling (SEM) indicated that temperature, salinity and total suspended substances along with nutrient availability, particulate carbon and Chl a, affected the distribution and co-occurrence of microbial groups, such as Actinobacteria, Bacteroidetes, Cyanobacteria, Planctomycetes, Proteobacteria, and Verrucomicrobia. Interestingly, compared to the abundant groups (such as SAR11, Saprospiraceae and Actinomarinaceae), the rare taxa including OM60 (NOR5) clade (Gammaproteobacteria), Micrococcales (Actinobacteria), and NS11-12 marine group (Bacteroidetes) contributed greatly to the stability of microbial co-occurrence in the Bay. Modularity and cluster structures of microbial networks varied spatiotemporally, which provided valuable insights into the 'small world' (a group of more interconnected species), network stability, and habitat partitioning/preferences. CONCLUSION Our results shed light on how estuarine gradients alter the spatiotemporal variations of prokaryotic microbial networks in the estuarine ecosystem, as well as their adaptability to environmental disturbances and co-occurrence network complexity and stability.
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Affiliation(s)
- Hualong Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD, USA
| | - Chuanlun Zhang
- Department of Ocean Science and Engineering, Southern University of Science and Technology, Shenzhen, People's Republic of China
- Shenzhen Key Laboratory of Marine Archaea Geo-Omics, Southern University of Science and Technology, Shenzhen, People's Republic of China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, China
| | - Min Wang
- College of Marine Life Sciences, and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Jinjun Kan
- Microbiology Division, Stroud Water Research Center, Avondale, PA, USA.
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, Shenzhen, People's Republic of China.
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95
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Hempel PP, Keffer JL, Maresca JA. RNA-Seq Reveals that Light and Darkness Are Different Stimuli in Freshwater Heterotrophic Actinobacteria. Front Microbiol 2021; 12:739005. [PMID: 34790178 PMCID: PMC8591293 DOI: 10.3389/fmicb.2021.739005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 10/11/2021] [Indexed: 01/20/2023] Open
Abstract
Light is a ubiquitous source of both energy and information in surface environments, and regulates gene expression not only in photosynthetic microorganisms, but in a broad range of photoheterotrophic and heterotrophic microbes as well. Actinobacteria are keystone species in surface freshwater environments, where the ability to sense light could allow them to coordinate periods of nutrient uptake and metabolic activity with primary production. The model freshwater Actinobacteria Rhodoluna (R.) lacicola strain MWH-Ta8 and Aurantimicrobium (A.) photophilum strain MWH-Mo1 grow faster in the light than in the dark, but do not use light energy to support growth. Here, we characterize transcription throughout a light-dark cycle in R. lacicola and A. photophilum. In both species, some genes encoding carbohydrate metabolism and storage are upregulated in the light. However, expression of genes of the TCA cycle is only coordinated with light availability in R. lacicola. In fact, the majority of genes that respond to light and darkness in these two species are different, even though their light-responsive phenotypes are similar. The ability to respond to light and darkness may be widespread in freshwater Actinobacteria, but the genetic networks controlled by these two stimuli may vary significantly.
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Affiliation(s)
- Priscilla P. Hempel
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States
| | - Jessica L. Keffer
- Department of Civil and Environmental Engineering, University of Delaware, Newark, DE, United States
| | - Julia A. Maresca
- Department of Civil and Environmental Engineering, University of Delaware, Newark, DE, United States
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96
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Zhang L, Li X, Fang W, Cheng Y, Cai H, Zhang S. Impact of different types of anthropogenic pollution on bacterial community and metabolic genes in urban river sediments. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 793:148475. [PMID: 34174597 DOI: 10.1016/j.scitotenv.2021.148475] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/11/2021] [Accepted: 06/11/2021] [Indexed: 06/13/2023]
Abstract
Sediment bacterial communities play a crucial role in the biogeochemical cycle of nutrient elements in urban river. However, the distribution of nitrogen cycle genes on bacterial communities in urban rivers sediments is largely unknown. Here, 16S rRNA amplicon sequencing was used to analyze the composition, co-occurrence patterns and nitrogen cycle process of bacterial communities in urban river sediments under the influence of different exogenous pollution. The results revealed that bacterial communities had significant spatial heterogeneity in river sediments of different polluted areas, and the input of different exogenous pollutants shaped the abundance and distribution of nitrogen cycle-related genes in the sediments. In addition, denitrification process played a leading role in the nitrogen cycle of river sediments, and the genes associated with the nitrification process were rarely observed in all samples. The important bacterial taxonomic biomarkers of nitrogen cycling-related genes screened by random forest algorithm were Synergistia, WS6_Dojkabacteria and Caldisericia. Meanwhile, different co-occurrence patterns observed in different types of polluted areas clarified the impact of environmental filtration and niche differentiation on bacterial communities. In conclusion, this study reveals the nitrogen cycle process and the distribution of related genes mediated by bacterial communities under the impact of different anthropogenic contamination, and provides novel insights for the assembly of bacterial communities in urban river sediments.
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Affiliation(s)
- Lei Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China.
| | - Xingchen Li
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China
| | - Wangkai Fang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China
| | - Yu Cheng
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China
| | - Hua Cai
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China
| | - Siqing Zhang
- School of Civil Engineering and Architecture, Chuzhou University, Chuzhou 239000, China
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97
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Fan H, Wu S, Dong W, Li X, Dong Y, Wang S, Zhu YG, Zhuang X. Characterization of tetracycline-resistant microbiome in soil-plant systems by combination of H 218O-based DNA-Stable isotope probing and metagenomics. JOURNAL OF HAZARDOUS MATERIALS 2021; 420:126440. [PMID: 34280721 DOI: 10.1016/j.jhazmat.2021.126440] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Revised: 06/16/2021] [Accepted: 06/18/2021] [Indexed: 05/12/2023]
Abstract
The emergence and spread of antibiotic resistance have been considered as a global health threat. However, effective methods to identify antibiotic-resistant bacteria (ARB) in complex microbial community are lacking, and the potential transmission pathways of ARB and antibiotic resistance genes (ARGs) in the soil-plant system remain scarce. Here in this study, tetracycline was chosen as the target antibiotic due to its globally wide usage and clinical significance. DNA-based stable isotope probing with H218O was applied to identify the tetracycline-resistant bacteria from soil-plant systems. Eighteen-year organic fertilization significantly changed the composition of the tetracycline-resistant microbiome in the soil-wheat system and resulted in a higher relative abundance of ARGs in the wheat endophyte. Rhizosphere harboring the most diverse ARGs and mobile genetic elements was identified as a hot spot for horizontal gene transfer and an important bridge between bulk soil and wheat endophyte. Micrococcaceae and Sphingomonadaceae carrying ARGs associated with abundant mobile genetic elements, were identified as the core bacterial taxa in long-term manure-amended and untreated soil-wheat systems, respectively. This method contributes to a more precise track of ARB in the environment, and our work depicts the high potential of ARG transfer in the rhizosphere mediated by the core species.
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Affiliation(s)
- Haonan Fan
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shanghua Wu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenxu Dong
- Key Laboratory of Agricultural Water Resources, Center for Agricultural Resources Research, Institute of Genetic and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xianglong Li
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuzhu Dong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shijie Wang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuliang Zhuang
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China.
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98
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Mayerhofer MM, Eigemann F, Lackner C, Hoffmann J, Hellweger FL. Dynamic carbon flux network of a diverse marine microbial community. ISME COMMUNICATIONS 2021; 1:50. [PMID: 37938646 PMCID: PMC9723560 DOI: 10.1038/s43705-021-00055-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 08/19/2021] [Accepted: 09/10/2021] [Indexed: 11/09/2023]
Abstract
The functioning of microbial ecosystems has important consequences from global climate to human health, but quantitative mechanistic understanding remains elusive. The components of microbial ecosystems can now be observed at high resolution, but interactions still have to be inferred e.g., a time-series may show a bloom of bacteria X followed by virus Y suggesting they interact. Existing inference approaches are mostly empirical, like correlation networks, which are not mechanistically constrained and do not provide quantitative mass fluxes, and thus have limited utility. We developed an inference method, where a mechanistic model with hundreds of species and thousands of parameters is calibrated to time series data. The large scale, nonlinearity and feedbacks pose a challenging optimization problem, which is overcome using a novel procedure that mimics natural speciation or diversification e.g., stepwise increase of bacteria species. The method allows for curation using species-level information from e.g., physiological experiments or genome sequences. The product is a mass-balancing, mechanistically-constrained, quantitative representation of the ecosystem. We apply the method to characterize phytoplankton-heterotrophic bacteria interactions via dissolved organic matter in a marine system. The resulting model predicts quantitative fluxes for each interaction and time point (e.g., 0.16 µmolC/L/d of chrysolaminarin to Polaribacter on April 16, 2009). At the system level, the flux network shows a strong correlation between the abundance of bacteria species and their carbon flux during blooms, with copiotrophs being relatively more important than oligotrophs. However, oligotrophs, like SAR11, are unexpectedly high carbon processors for weeks into blooms, due to their higher biomass. The fraction of exudates (vs. grazing/death products) in the DOM pool decreases during blooms, and they are preferentially consumed by oligotrophs. In addition, functional similarity of phytoplankton i.e., what they produce, decouples their association with heterotrophs. The methodology is applicable to other microbial ecosystems, like human microbiome or wastewater treatment plants.
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Affiliation(s)
| | - Falk Eigemann
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Carsten Lackner
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Jutta Hoffmann
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany
| | - Ferdi L Hellweger
- Water Quality Engineering, Technical University of Berlin, Berlin, Germany.
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99
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Li A, Li Z, Dai W, Parise KL, Leng H, Jin L, Liu S, Sun K, Hoyt JR, Feng J. Bacterial community dynamics on bats and the implications for pathogen resistance. Environ Microbiol 2021; 24:1484-1498. [PMID: 34472188 DOI: 10.1111/1462-2920.15754] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 07/07/2021] [Accepted: 08/30/2021] [Indexed: 02/02/2023]
Abstract
The bats skin microbiota plays an important role in reducing pathogen infection, including the deadly fungal pathogen Pseudogymnoascus destructans, the causative agent of white-nose syndrome. However, the dynamic of skin bacterial communities response to environmental perturbations remains poorly described. We characterized skin bacterial community over time and space in Rhinolophus ferrumequinum, a species with high resistance to the infection with P. destructans. We collected environmental covariate data to determine what factors influenced changes in community structure. We observed significant temporal and spatial shifts in the skin bacterial community, which was mainly associated with variation in operational taxonomic units. The skin bacterial community differed by the environmental microbial reservoirs and was most influenced by host body condition, bat roosting temperature and geographic distance between sites, but was not influenced by pathogen infection. Furthermore, the skin microbiota was enriched in particular taxa with antifungal abilities, such as Enterococcus, Burkholderia, Flavobacterium, Pseudomonas, Corynebacterium and Rhodococcus. And specific strains of Pseudomonas, Corynebacterium and Rhodococcus even inhibited P. destructans growth. Our findings provide new insights in characterizing the variation in bacterial communities can inform us about the processes of driving community assembly and predict the host's ability to resist or survive pathogen infection.
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Affiliation(s)
- Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.,Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun, 130024, China
| | - Zhongle Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.,College of Animal Science and Technology, Jilin Agricultural University, Changchun, 130118, China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Katy L Parise
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Longru Jin
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Sen Liu
- College of Life Sciences, Henan Normal University, Xinxiang, 453007, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China
| | - Joseph R Hoyt
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, VA, 24060, USA
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, 2555 Jingyue Street, Changchun, 130117, China.,College of Life Science, Jilin Agricultural University, Changchun, 130118, China
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100
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Brasell KA, Howarth J, Pearman JK, Fitzsimons SJ, Zaiko A, Pochon X, Vandergoes MJ, Simon K, Wood SA. Lake microbial communities are not resistant or resilient to repeated large-scale natural pulse disturbances. Mol Ecol 2021; 30:5137-5150. [PMID: 34379827 DOI: 10.1111/mec.16110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 07/16/2021] [Accepted: 07/27/2021] [Indexed: 11/28/2022]
Abstract
Opportunities to study community level responses to extreme natural pulse disturbances in unaltered ecosystems are rare. Lake sediment records that span thousands of years can contain well resolved sediment pulses, triggered by earthquakes. These paleo-records provide a means to study repeated pulse disturbance and processes of resistance (insensitivity to disturbance) and ecological resilience (capacity to regain structure, function and process). In this study, sedimentary DNA was extracted from a sediment core from Lake Paringa (New Zealand) that is situated in a near natural catchment. Metabarcoding and inferred functions were used to assess the lake microbial community over the past 1,100 years - a period that included four major earthquakes. Microbial community composition and function differed significantly between highly perturbed (postseismic, c. 50 yrs) phases directly after the earthquakes and more stable (interseismic, c. 250 yr) phases, indicating a lack of community resistance. Although community structure differed significantly in successive postseismic phases, function did not, suggesting potential functional redundancy. Significant differences in composition and function in successive interseismic phases demonstrates communities are not resilient to large-scale natural pulse disturbances. The clear difference in structure and function, and high number of indicator taxa (responsible for driving differences in communities between phases) in the fourth interseismic phase likely represents a regime shift, possibly due to the two-fold increase in sediment and terrestrial biospheric organic carbon fluxes recorded following the fourth earthquake. Large pulse disturbances that enhance sediment inputs into lake systems may produce an underappreciated mechanism that destabilises lake ecosystem processes.
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Affiliation(s)
- Katie A Brasell
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | | | - John K Pearman
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
| | | | - Anastasija Zaiko
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | - Xavier Pochon
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand.,University of Auckland, Auckland, New Zealand
| | | | - Kevin Simon
- University of Auckland, Auckland, New Zealand
| | - Susanna A Wood
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
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