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Li H, Cai L, Wang L, Wang Y, Xu J, Zhang R. The structure and assembly mechanisms of T4-like cyanophages community in the South China Sea. Microbiol Spectr 2024; 12:e0200223. [PMID: 38193726 PMCID: PMC10846272 DOI: 10.1128/spectrum.02002-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 11/27/2023] [Indexed: 01/10/2024] Open
Abstract
Marine ecosystems contain an immense diversity of phages, many of which infect cyanobacteria (cyanophage) that are largely responsible for primary productivity. To characterize the genetic diversity and biogeographic distribution of the marine T4-like cyanophage community in the northern South China Sea, the T4-like cyanophage portal protein gene (g20) was amplified. Phylogenetic analysis revealed that marine T4-like cyanophages were highly diverse, with g20 operational taxonomic units being affiliated with five defined clades (Clusters I-V). Cluster II had a wide geographic distribution, Cluster IV was the most abundant in the open sea, and Cluster I was dominant in coastal shelf environments. Our results showed T4-like cyanophages (based on g20) community was generally shaped via heterogeneous selection. Highly variable environmental factors (such as salinity and temperature) can heterogeneously select different cyanophage communities. Nevertheless, the dominant drivers of the T4-like cyanophage community based on the g20 and g23 (T4-like phage major capsid protein gene) were different, probably due to different coverages by the primer sets. Furthermore, the community assembly processes of T4-like cyanophages were affected by host traits (abundance and distribution), viral traits (latent period, burst size, and host range), and environmental properties (temperature and salinity).IMPORTANCECyanophages are abundant and ubiquitous in the oceans, altering population structures and evolution of cyanobacteria, which account for a large portion of global carbon fixation, through host mortality, horizontal gene transfer, and the modulation of host metabolism. However, little is known about the biogeography and ecological drivers that shape the cyanophage community. Here, we use g20 and g23 genes to examine the biogeographic patterns and the assembly mechanisms of T4-like cyanophage community in the northern part of the South China Sea. The different coverages of primer sets might lead to the different dominant drivers of T4-like cyanophage community based on g20 and g23 genes. Our results showed that characteristics of viral traits (latent period, burst size, and host range) and host traits (abundance and distribution) were found to either limit or enhance the biogeographic distribution of T4-like cyanophages. Overall, both virus and host properties are critical to consider when determining rules of community assembly for viruses.
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Affiliation(s)
- Huifang Li
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lanlan Cai
- Department of Ocean Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yu Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Juntian Xu
- Jiangsu Institute of Marine Resources Development, Jiangsu Ocean University, Lianyungang, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
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2
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Wang R, Xu S, Zhu Y, Zhang T, Ge S. Denitrifying anaerobic methane-oxidizing bacteria in river networks of the Taihu Basin: Community dynamics and assembly process. Front Microbiol 2022; 13:1074316. [PMID: 36605517 PMCID: PMC9808034 DOI: 10.3389/fmicb.2022.1074316] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 11/25/2022] [Indexed: 12/24/2022] Open
Abstract
Denitrifying anaerobic methane-oxidizing bacteria (DAMO bacteria) plays an important role in reducing methane emissions from river ecosystems. However, the assembly process of their communities underlying different hydrologic seasons remains unclarified. In this study, the dynamics of DAMO bacterial communities in river networks of the Taihu Basin were investigated by amplicon sequencing across wet, normal, and dry seasons followed by multiple statistical analyses. Phylogenetic analysis showed that Group B was the major subgroup of DAMO bacteria and significant dynamics for their communities were observed across different seasons (constrained principal coordinate analysis, p = 0.001). Furthermore, the neutral community model and normalized stochasticity ratio model were applied to reveal the underlying assembly process. Stochastic process and deterministic process dominated the assembly process in wet season and normal season, respectively and similar contributions of deterministic and stochastic processes were observed in dry season. Meanwhile, abundant (relative abundance >0.1%) and rare (relative abundance <0.01%) DAMO bacterial communities were found to be shaped via distinct assembly processes. Deterministic and stochastic processes played a considerable role in shaping abundant DAMO bacterial communities, while deterministic process mainly shaped rare DAMO bacterial communities. Results of this study revealed the dynamics of DAMO bacterial communities in river networks and provided a theoretical basis for further understanding of the assembly process.
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Affiliation(s)
- Ruyue Wang
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China
| | - Sai Xu
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China,*Correspondence: Sai Xu,
| | - Yuxiang Zhu
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, China
| | - Tao Zhang
- Nanjing Institute of Environmental Sciences, Ministry of Ecology and Environment, Nanjing, China
| | - Shijian Ge
- Jiangsu Key Laboratory of Chemical Pollution Control and Resources Reuse, School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, China,Shijian Ge,
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3
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Gronniger JL, Wang Z, Brandt GR, Ward CS, Tsementzi D, Mu H, Gu J, Johnson ZI, Konstantinidis KT, Hunt DE. Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables. Environ Microbiol 2022; 24:4167-4177. [PMID: 35715385 DOI: 10.1111/1462-2920.16086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 05/25/2022] [Indexed: 11/30/2022]
Abstract
Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week-over-week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage-associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re-examined in the context of ecological history and microbiome responses.
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Affiliation(s)
| | - Zhao Wang
- Marine Laboratory, Duke University, Beaufort, NC, USA
| | | | | | | | - Han Mu
- Marine Laboratory, Duke University, Beaufort, NC, USA
| | - Junyao Gu
- Marine Laboratory, Duke University, Beaufort, NC, USA
| | - Zackary I Johnson
- Marine Laboratory, Duke University, Beaufort, NC, USA.,Biology and Civil & Environmental Engineering, Duke University, Durham, NC, USA
| | | | - Dana E Hunt
- Marine Laboratory, Duke University, Beaufort, NC, USA.,Biology and Civil & Environmental Engineering, Duke University, Durham, NC, USA
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4
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Courcoul C, Leflaive J, Ferriol J, Boulêtreau S. The sensitivity of aquatic microbial communities to a complex agricultural contaminant depends on previous drought conditions. WATER RESEARCH 2022; 217:118396. [PMID: 35413563 DOI: 10.1016/j.watres.2022.118396] [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: 01/08/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 06/14/2023]
Abstract
In intermittent rivers, which represent a prominent part of worldwide rivers, aquatic organisms are exposed to sequential disturbances including flow cessation, potentially associated with water warming, desiccation process and flow resumption. At flow resumption, pollutants stored in soil and washed by rainfalls can reach fresh waters. The interaction between contamination and river intermittency is poorly understood. In this study, we aimed at understanding in what extent the intensity of dry period combined or not to water warming drives the sensitivity of aquatic communities to a complex agricultural run-off (ARO) during rewetting. Phototrophic biofilms, at the basis of freshwater food webs, were chosen as a model of community. Biofilms grown in laboratory were first exposed to a disturbance crossing two temperature conditions (not warmed, 22°C or warmed, 32°C) and three dry periods (no drying, short (3 days), or long (3 months)). Then they were exposed to a chemical mix of nitrates, copper and 3 pesticides at 6 gradual concentrations. Various descriptors associated with biofilm structure and function were assessed one week after ARO addition. When undisturbed biofilms were exposed to ARO, they shifted toward a more heterotrophic state as they lost algal richness and diversity, and gross primary production tended to decrease. Warming alone only slightly modified the sensitivity of biofilms to ARO, with lower effects on algal richness and a trend to increase the effect on gross primary production. In contrast, the association of warming and a dry period strongly modified the sensitivity to ARO, certainly due to the selection of generalist species and/or physiological acclimation inducted by the first disturbance. This study emphasizes the importance of considering water intermittency in the management of the ecological risk of chemicals in aquatic ecosystems.
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Affiliation(s)
- Camille Courcoul
- Laboratoire d'Ecologie Fonctionnelle et Environnement de Toulouse, Université de Toulouse, CNRS UMR 5245, INPT, UPS, Toulouse, France.
| | - Joséphine Leflaive
- Laboratoire d'Ecologie Fonctionnelle et Environnement de Toulouse, Université de Toulouse, CNRS UMR 5245, INPT, UPS, Toulouse, France
| | - Jessica Ferriol
- Laboratoire d'Ecologie Fonctionnelle et Environnement de Toulouse, Université de Toulouse, CNRS UMR 5245, INPT, UPS, Toulouse, France
| | - Stéphanie Boulêtreau
- Laboratoire d'Ecologie Fonctionnelle et Environnement de Toulouse, Université de Toulouse, CNRS UMR 5245, INPT, UPS, Toulouse, France
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Ansari MI, Calleja MLI, Silva L, Viegas M, Ngugi DK, Huete-Stauffer TM, Morán XAG. High-Frequency Variability of Bacterioplankton in Response to Environmental Drivers in Red Sea Coastal Waters. Front Microbiol 2022; 13:780530. [PMID: 35432231 PMCID: PMC9009512 DOI: 10.3389/fmicb.2022.780530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 03/03/2022] [Indexed: 11/13/2022] Open
Abstract
Autotrophic and heterotrophic bacterioplankton are essential to the biogeochemistry of tropical ecosystems. However, the processes that govern their dynamics are not well known. We provide here a high-frequency assessment of bacterial community dynamics and concurrent environmental factors in Red Sea coastal waters. Weekly sampling of surface samples during a full annual cycle at an enclosed station revealed high variability in ecological conditions, which reflected in changes of major bacterioplankton communities. Temperature varied between 23 and 34°C during the sampling period. Autotrophic (Synechococcus, 1.7–16.2 × 104 cells mL−1) and heterotrophic bacteria (1.6–4.3 × 105 cells mL−1) showed two maxima in abundance in spring and summer, while minima were found in winter and autumn. Heterotrophic cells with high nucleic acid content (HNA) peaked in July, but their contribution to the total cell counts (35–60%) did not show a clear seasonal pattern. Actively respiring cells (CTC+) contributed between 4 and 51% of the total number of heterotrophic bacteria, while live cells (with intact membrane) consistently accounted for over 90%. Sequenced 16S rRNA amplicons revealed a predominance of Proteobacteria in summer and autumn (>40%) and a smaller contribution in winter (21–24%), with members of the Alphaproteobacteria class dominating throughout the year. The contribution of the Flavobacteriaceae family was highest in winter (21%), while the Rhodobacteraceae contribution was lowest (6%). Temperature, chlorophyll-a, and dissolved organic carbon concentration were the environmental variables with the greatest effects on bacterial abundance and diversity patterns.
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Affiliation(s)
- Mohd Ikram Ansari
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Biosciences, Integral University, Lucknow, India
- *Correspondence: Mohd Ikram Ansari, ; Xosé Anxelu G. Morán,
| | - Maria LI. Calleja
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Climate Geochemistry, Max Planck Institute for Chemistry (MPIC), Mainz, Germany
| | - Luis Silva
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Miguel Viegas
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - David Kamanda Ngugi
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Department of Microorganisms, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Tamara Megan Huete-Stauffer
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Xosé Anxelu G. Morán
- Division of Biological and Environmental Sciences and Engineering (BESE), Red Sea Research Center (RSRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- Centro Oceanográfico de Gijón/Xixón (IEO, CSIC), Gijón/Xixón, Spain
- *Correspondence: Mohd Ikram Ansari, ; Xosé Anxelu G. Morán,
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Potts L, Douglas A, Perez Calderon LJ, Anderson JA, Witte U, Prosser JI, Gubry-Rangin C. Chronic Environmental Perturbation Influences Microbial Community Assembly Patterns. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:2300-2311. [PMID: 35103467 PMCID: PMC9007448 DOI: 10.1021/acs.est.1c05106] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Acute environmental perturbations are reported to induce deterministic microbial community assembly, while it is hypothesized that chronic perturbations promote development of alternative stable states. Such acute or chronic perturbations strongly impact on the pre-adaptation capacity to the perturbation. To determine the importance of the level of microbial pre-adaptation and the community assembly processes following acute or chronic perturbations in the context of hydrocarbon contamination, a model system of pristine and polluted (hydrocarbon-contaminated) sediments was incubated in the absence or presence (discrete or repeated) of hydrocarbon amendment. The community structure of the pristine sediments changed significantly following acute perturbation, with selection of different phylotypes not initially detectable. Conversely, historically polluted sediments maintained the initial community structure, and the historical legacy effect of chronic pollution likely facilitated community stability. An alternative stable state was also reached in the pristine sediments following chronic perturbation, further demonstrating the existence of a legacy effect. Finally, ecosystem functional resilience was demonstrated through occurrence of hydrocarbon degradation by different communities in the tested sites, but the legacy effect of perturbation also strongly influenced the biotic response. This study therefore demonstrates the importance of perturbation chronicity on microbial community assembly processes and reveals ecosystem functional resilience following environmental perturbation.
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Affiliation(s)
- Lloyd
D. Potts
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Alex Douglas
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Luis J. Perez Calderon
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James A. Anderson
- Materials
and Chemical Engineering, School of Engineering, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Ursula Witte
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - James I. Prosser
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
| | - Cécile Gubry-Rangin
- School
of Biological Sciences, University of Aberdeen, Aberdeen AB24 3FX, U.K.
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7
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Wu Y, Wu J, Wu Z, Zhou J, Zhou L, Lu Y, Liu X, Wu W. Groundwater contaminated with short-chain chlorinated paraffins and microbial responses. WATER RESEARCH 2021; 204:117605. [PMID: 34488140 DOI: 10.1016/j.watres.2021.117605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 08/21/2021] [Accepted: 08/23/2021] [Indexed: 06/13/2023]
Abstract
The vertical migrations of toxic and persistent short-chain chlorinated paraffins (SCCPs) in soils as well as the microbial responses have been reported, however, there is a paucity of data on the resulting groundwater contamination. Here, we determined the concentration and congener profile of SCCPs in the groundwater beneath a production plant of chlorinated paraffins (CPs) and characterized the microbial community to explore their responses to SCCPs. Results showed that SCCPs ranged from not detected to 70.3 μg/L, with C13-CPs (11.2-65.8%) and Cl7-CPs (27.2-50.6%), in mass ratio, as the dominant groups. Similar to the distribution pattern in soils, SCCPs in groundwater were distributed in hotspot pattern. CP synthesis was the source of SCCPs in groundwater and the entire contamination plume significantly migrated downgradient, while there was an apparent hysteresis of C13-CP migration. Groundwater microbial community was likely shaped by both hydrogeological condition (pH and depth) and SCCPs. Specifically, the microbial community responded to the contamination by forming a co-occurrence network with "small world" feature, where Desulfobacca, Desulfomonile, Ferritrophicum, Methylomonas, Syntrophobacter, Syntrophorhabdus, Syntrophus, and Thermoanaerobaculum were the keystone taxa. Furthermore, the interrelations between bacterial taxa and SCCPs indicated that the microbial community might cooperate to achieve the dechlorination and mineralization of SCCPs through either anaerobic organohalide respiration mainly functioned by the keystone taxa, or cometabolic degradation processes functioned by Aquabacterium and Hydrogenophaga. Results of this study would provide a better understanding of the environmental behavior and ecological effects of SCCPs in groundwater systems.
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Affiliation(s)
- Yingxin Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Jiahui Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Zhuohao Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Jingyan Zhou
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Lingli Zhou
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Yang Lu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Xiaowen Liu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China
| | - Wencheng Wu
- South China Institute of Environmental Sciences, Ministry of Ecology and Environment, 7 West Street, Yuancun, Guangzhou 510655, PR China.
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8
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Microbial Community Resilience across Ecosystems and Multiple Disturbances. Microbiol Mol Biol Rev 2021; 85:85/2/e00026-20. [PMID: 33789927 DOI: 10.1128/mmbr.00026-20] [Citation(s) in RCA: 76] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The ability of ecosystems to withstand disturbances and maintain their functions is being increasingly tested as rates of change intensify due to climate change and other human activities. Microorganisms are crucial players underpinning ecosystem functions, and the recovery of microbial communities from disturbances is therefore a key part of the complex processes determining the fate of ecosystem functioning. However, despite global environmental change consisting of numerous pressures, it is unclear and controversial how multiple disturbances affect microbial community stability and what consequences this has for ecosystem functions. This is particularly the case for those multiple or compounded disturbances that occur more frequently than the normal recovery time. The aim of this review is to provide an overview of the mechanisms that can govern the responses of microbes to multiple disturbances across aquatic and terrestrial ecosystems. We first summarize and discuss properties and mechanisms that influence resilience in aquatic and soil biomes to determine whether there are generally applicable principles. Following, we focus on interactions resulting from inherent characteristics of compounded disturbances, such as the nature of the disturbance, timing, and chronology that can lead to complex and nonadditive effects that are modulating the response of microorganisms.
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9
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Rathore DS, Sheikh MA, Gohel SD, Singh SP. Genetic and Phenotypic Heterogeneity of the Nocardiopsis alba Strains of Seawater. Curr Microbiol 2021; 78:1377-1387. [PMID: 33646381 DOI: 10.1007/s00284-021-02420-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 02/10/2021] [Indexed: 11/29/2022]
Abstract
This study deals with the genetic and phenotypic heterogeneity of the marine Nocardiopsis alba strains isolated during pre-monsoon, monsoon and post-monsoon seasons. The isolates were characterized for their morphological and biochemical attributes, growth media preferences, antibiotic susceptibility and extracellular enzyme secretion. Nocardiopsis alba strains were assessed against 12 different antibiotics, and the responses were expressed in terms of the multiple antibiotic resistance (MAR) number. The majority of the strains produced multiple extracellular enzymes: proteases, amylases and lipases. Further, the strains were characterized on the basis of 16S rRNA gene sequencing and the majority were identified as Nocardiopsis alba along with few strains of Streptomyces lopnurensis, Nocardiopsis synnemataformans and Nocardiopsis dassonvillei. Neighbor-joining (NJ) phylogenetic tree suggested variation among the genetically similar Nocardiopsis alba species. The study establishes significant heterogeneity with respect to genetic and phenotypic characteristics of the strains of Nocardiopsis alba. Phylogenetic tree and phenogram-based comparison reflect the heterogeneity in terms of different clustering patterns of the strains. Further, the whole genome sequence data available in the literature also confirm the observed heterogeneity. Nocardiopsis alba strains displayed a relatively regressive pattern of dependence on the environmental factors based on the canonical correspondence analysis plot. The study represents cultivation, characterization, phylogenetic analysis and enzymatic potential of the Nocardiopsis alba species of seawater origin.
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Affiliation(s)
- Dalip Singh Rathore
- Department of Biosciences, UGC Centre for Advanced Studies (CAS), Saurashtra University, Rajkot, Gujarat, India
| | - Mahejbin A Sheikh
- Department of Biosciences, UGC Centre for Advanced Studies (CAS), Saurashtra University, Rajkot, Gujarat, India
| | - Sangeeta D Gohel
- Department of Biosciences, UGC Centre for Advanced Studies (CAS), Saurashtra University, Rajkot, Gujarat, India
| | - Satya P Singh
- Department of Biosciences, UGC Centre for Advanced Studies (CAS), Saurashtra University, Rajkot, Gujarat, India.
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10
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Coclet C, Garnier C, Durrieu G, D'onofrio S, Layglon N, Briand JF, Misson B. Impacts of copper and lead exposure on prokaryotic communities from contaminated contrasted coastal seawaters: the influence of previous metal exposure. FEMS Microbiol Ecol 2020; 96:5809961. [PMID: 32188980 DOI: 10.1093/femsec/fiaa048] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 03/17/2020] [Indexed: 01/04/2023] Open
Abstract
Our understanding of environmental factors controlling prokaryotic community is largely hampered by the large environmental variability across spatial scales (e.g. trace metal contamination, nutrient enrichment and physicochemical variations) and the broad diversity of bacterial pre-exposure to environmental factors. In this article, we investigated the specific influence of copper (Cu) and lead (Pb) on prokaryotic communities from the uncontaminated site, using mesocosm experiments. In addition, we studied how pre-exposure (i.e. life history) affects communities, with reference to previous metal exposure on the response of three prokaryotic communities to similar Cu exposition. This study showed a stronger influence of Cu contamination than Pb contamination on prokaryotic diversity and structure. We identified 12 and 34 bacterial families and genera, respectively, contributing to the significant differences observed in community structure between control and spiked conditions. Taken altogether, our results point toward a combination of direct negative responses to Cu contamination and indirect responses mediated by interaction with phytoplankton. These identified responses were largely conditioned by the previous exposure of community to contaminants.
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Affiliation(s)
- Clément Coclet
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 83041 Toulon, Cedex 9, Franc.,Université de Toulon, MAPIEM, EA 4323, Toulon, 83041 Toulon, Cedex 9, Franc
| | - Cédric Garnier
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 83041 Toulon, Cedex 9, Franc
| | - Gaël Durrieu
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 83041 Toulon, Cedex 9, Franc
| | - Sébastien D'onofrio
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 83041 Toulon, Cedex 9, Franc
| | - Nicolas Layglon
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 83041 Toulon, Cedex 9, Franc
| | | | - Benjamin Misson
- Université de Toulon, Aix Marseille Université, CNRS, IRD, Mediterranean Institute of Oceanography (MIO), UM 110, 83041 Toulon, Cedex 9, Franc
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11
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Yang M, Shi J, Wang B, Xiao J, Li W, Liu CQ. Control of Hydraulic Load on Bacterioplankton Diversity in Cascade Hydropower Reservoirs, Southwest China. MICROBIAL ECOLOGY 2020; 80:537-545. [PMID: 32462390 DOI: 10.1007/s00248-020-01523-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 05/05/2020] [Indexed: 05/25/2023]
Abstract
Hydroelectric reservoirs are highly regulated ecosystems, where the understanding on bacterioplankton has been very limited so far. In view of significant changes in river hydrological conditions by dam construction, hydraulic load (i.e., the ratio of mean water depth to water retention time) was assumed to control bacterioplankton diversity in cascading hydropower reservoirs. To evaluate this hypothesis, we investigated bacterioplankton composition and diversity using high-throughput sequencing and related environmental variables in eleven reservoirs on the Wujiang River, Southwest China. Our results showed a decrease of bacterioplankton diversity index with an increase of reservoir hydraulic load. This is because hydraulic load governs dissolved oxygen variation in the water column, which is a key factor shaping bacterioplankton composition in these hydroelectric reservoirs. In contrast, bacterioplankton abundance was mainly affected by nutrient-related environmental factors. Therefore, from a hydrological perspective, hydraulic load is a decisive factor for the bacterioplankton diversity in the hydroelectric reservoirs. This study can improve the understanding of reservoir bacterial ecology, and the empirical relationship between hydraulic load and bacterioplankton diversity index will help to quantitatively evaluate ecological effects of river damming.
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Affiliation(s)
- Meiling Yang
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Jie Shi
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Baoli Wang
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China.
| | - Jing Xiao
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Wanzhu Li
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
| | - Cong-Qiang Liu
- Institute of Surface-Earth System Science, Tianjin University, Tianjin, 300072, China
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12
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Renes SE, Sjöstedt J, Fetzer I, Langenheder S. Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances. Sci Rep 2020; 10:11333. [PMID: 32647292 PMCID: PMC7347917 DOI: 10.1038/s41598-020-68104-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 06/18/2020] [Indexed: 02/08/2023] Open
Abstract
Climate change is expected to increase the incidences of extremes in environmental conditions. To investigate how repeated disturbances affect microbial ecosystem resistance, natural lake bacterioplankton communities were subjected to repeated temperature disturbances of two intensities (25 °C and 35 °C), and subsequently to an acidification event. We measured functional parameters (bacterial production, abundance, extracellular enzyme activities) and community composition parameters (richness, evenness, niche width) and found that, compared to undisturbed control communities, the 35 °C treatment was strongly affected in all parameters, while the 25 °C treatment did not significantly differ from the control. Interestingly, exposure to multiple temperature disturbances caused gradually increasing stability in the 35 °C treatment in some parameters, while others parameters showed the opposite, indicating that the choice of parameters can strongly affect the outcome of a study. The acidification event did not lead to stronger changes in community structure, but functional resistance of bacterial production towards acidification in the 35 °C treatments increased. This indicates that functional resistance in response to a novel disturbance can be increased by previous exposure to another disturbance, suggesting similarity in stress tolerance mechanisms for both disturbances. These results highlight the need for understanding function- and disturbance-specific responses, since general responses are likely to be unpredictable.
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Affiliation(s)
- Sophia Elise Renes
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, Sweden. .,Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden.
| | - Johanna Sjöstedt
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden. .,Department of Biology/Aquatic Ecology, Lund University, Lund, Sweden.
| | - Ingo Fetzer
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden.,Bolin Centre for Climate Research, Stockholm University, Stockholm, Sweden
| | - Silke Langenheder
- Department of Ecology and Genetics/Limnology, Uppsala University, Uppsala, Sweden
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13
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Huang L, Bai J, Wen X, Zhang G, Zhang C, Cui B, Liu X. Microbial resistance and resilience in response to environmental changes under the higher intensity of human activities than global average level. GLOBAL CHANGE BIOLOGY 2020; 26:2377-2389. [PMID: 31943531 DOI: 10.1111/gcb.14995] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/20/2019] [Accepted: 12/17/2019] [Indexed: 06/10/2023]
Abstract
With the increasing intensity of global human activities, the ecosystem function, which is supported by the microbial community, will be dramatically changed and impaired. To investigate microbial resistance and resilience of microbial communities to human activities, we chose two typical types of human disturbances, urbanization, and reclamation under the higher intensity of human activities than the global average level. We examined microbial traits, including the abundance, diversity, phylogeny, and co-occurrence interactions in soil microbial communities, together with the nitrification activities observed in the subtropical coastal ecosystem of the Pearl River Estuary and in soil microcosm experiments. Microbial communities were less resistant to the environmental changes caused by urbanization than to those caused by reclamation, which was significantly reflected in the nitrogen and/or carbon-related patterns. However, most of the microbial traits could be recovered almost to the original level without significant differences in the microcosm after 40 days of incubation. The co-occurrence interactions between nitrifiers and other microbial communities were dramatically changed and could not be completely recovered, but this change did not affect their nitrification activities for balancing the ammonium in the soil to the original level during the recovery stage, suggesting that the interactions between microbial communities might have fewer effects on their activities than previously thought. This study quantitatively demonstrated that microbial communities as a whole can recover to a status similar to the original state in a short time after the removal of stress at a large ecosystem scale even under the higher intensity of human activities than global average level in coastal ecosystems, which implied a strong recovery capacity of soil microbial community even after intense human disturbance.
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Affiliation(s)
- Laibin Huang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Junhong Bai
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xiaojun Wen
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Guangliang Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Chengdong Zhang
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Baoshan Cui
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
| | - Xinhui Liu
- State Key Laboratory of Water Environment Simulation, School of Environment, Beijing Normal University, Beijing, China
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14
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Coclet C, Garnier C, Durrieu G, Omanović D, D’Onofrio S, Le Poupon C, Mullot JU, Briand JF, Misson B. Changes in Bacterioplankton Communities Resulting From Direct and Indirect Interactions With Trace Metal Gradients in an Urbanized Marine Coastal Area. Front Microbiol 2019; 10:257. [PMID: 30853948 PMCID: PMC6395402 DOI: 10.3389/fmicb.2019.00257] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 01/31/2019] [Indexed: 01/21/2023] Open
Abstract
Unraveling the relative importance of both environmental conditions and ecological processes regulating bacterioplankton communities is a central goal in microbial ecology. Marine coastal environments are among the most urbanized areas and as a consequence experience environmental pressures. The highly anthropized Toulon Bay (France) was considered as a model system to investigate shifts in bacterioplankton communities along natural and anthropogenic physicochemical gradients during a 1-month survey. In depth geochemical characterization mainly revealed strong and progressive Cd, Zn, Cu, and Pb contamination gradients between the entrance of the Bay and the north-western anthropized area. On the other hand, low-amplitude natural gradients were observed for other environmental variables. Using 16S rRNA gene sequencing, we observed strong spatial patterns in bacterioplankton taxonomic and predicted function structure along the chemical contamination gradient. Variation partitioning analysis demonstrated that multiple metallic contamination explained the largest part of the spatial biological variations observed, but DOC and salinity were also significant contributors. Network analysis revealed that biotic interactions were far more numerous than direct interactions between microbial groups and environmental variables. This suggests indirect effects of the environment, and especially trace metals, on the community through a few taxonomic groups. These spatial patterns were also partially found for predicted bacterioplankton functions, thus indicating a limited functional redundancy. All these results highlight both potential direct influences of trace metals contamination on coastal bacterioplankton and indirect forcing through biotic interactions and cascading.
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Affiliation(s)
- Clément Coclet
- Mediterranean Institute of Oceanography (MIO), UM110, CNRS, IRD, Université de Toulon, Aix-Marseille Université, Marseille, France
- MAPIEM, EA 4323, Université de Toulon, Toulon, France
| | - Cédric Garnier
- Mediterranean Institute of Oceanography (MIO), UM110, CNRS, IRD, Université de Toulon, Aix-Marseille Université, Marseille, France
| | - Gaël Durrieu
- Mediterranean Institute of Oceanography (MIO), UM110, CNRS, IRD, Université de Toulon, Aix-Marseille Université, Marseille, France
| | - Dario Omanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Zagreb, Croatia
| | - Sébastien D’Onofrio
- Mediterranean Institute of Oceanography (MIO), UM110, CNRS, IRD, Université de Toulon, Aix-Marseille Université, Marseille, France
| | - Christophe Le Poupon
- Mediterranean Institute of Oceanography (MIO), UM110, CNRS, IRD, Université de Toulon, Aix-Marseille Université, Marseille, France
| | | | | | - Benjamin Misson
- Mediterranean Institute of Oceanography (MIO), UM110, CNRS, IRD, Université de Toulon, Aix-Marseille Université, Marseille, France
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