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Palmer J, Bugnot AB, Filippini G, Gribben PE, Varkey D, Erickson K, Dafforn KA. The influence of bioturbator activity on sediment bacterial structure and function is moderated by environment. MARINE ENVIRONMENTAL RESEARCH 2024; 201:106702. [PMID: 39213892 DOI: 10.1016/j.marenvres.2024.106702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 08/04/2024] [Accepted: 08/18/2024] [Indexed: 09/04/2024]
Abstract
Bioturbation in coastal sediments plays a crucial role in biogeochemical cycling. However, a key knowledge gap is the extent to which bioturbation influences bacterial community diversity and ecosystem processes, such as nitrogen cycling. This study paired bacterial diversity, bioturbation activity and in situ flux measurements of oxygen and nitrogen from bioturbated sediments at six estuaries along the East coast of Australia. Bacterial community diversity, composition and predicted functional profiles were similar across burrow and surface sediments but were significantly influenced by bioturbator activity (measured as number of burrows) at sites with higher fine grain content. Sediment oxygen demand increased with bioturbator activity but changes in nitrogen cycling (as measured by fluxes and predicted bacterial functional gene analysis) were more spatially variable and were unrelated to bioturbator activity and bacterial community shifts. This study highlights how bioturbator activity influences bacterial community structure and functioning and what implications this has for biogeochemical cycles in estuarine sediments.
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Affiliation(s)
- Julia Palmer
- School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia.
| | - Ana B Bugnot
- School of Life and Environmental Sciences, The University of Sydney, Sydney, New South Wales, Australia; CSIRO Environment, Commonwealth Scientific and Industrial Research Organisation, St Lucia, QLD, 4067, Australia
| | - Giulia Filippini
- School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia; Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Paul E Gribben
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Deepa Varkey
- School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia
| | - Katherine Erickson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Katherine A Dafforn
- School of Natural Sciences, Macquarie University, North Ryde, NSW, Australia; Sydney Institute of Marine Science, Mosman, New South Wales, Australia
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2
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Gao SM, Wang P, Li Q, Shu WS, Tang LY, Lin ZL, Li JT, Huang LN. Deciphering microbial metabolic interactions and their implications for community dynamics in acid mine drainage sediments. JOURNAL OF HAZARDOUS MATERIALS 2024; 478:135478. [PMID: 39137550 DOI: 10.1016/j.jhazmat.2024.135478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 07/28/2024] [Accepted: 08/08/2024] [Indexed: 08/15/2024]
Abstract
The microbially-mediated reduction processes have potential for the bioremediation of acid mine drainage (AMD), which represents a worldwide environment problem. However, we know little about the microbial interactions in anaerobic AMD sediments. Here we utilized genome-resolved metagenomics to uncover the nature of cooperative and competitive metabolic interactions in 90 AMD sediments across Southern China. Our analyses recovered well-represented prokaryotic communities through the reconstruction of 2625 population genomes. Functional analyses of these genomes revealed extensive metabolic handoffs which occurred more frequently in nitrogen metabolism than in sulfur metabolism, as well as stable functional redundancy across sediments resulting from populations with low genomic relatedness. Genome-scale metabolic modeling showed that metabolic competition promoted microbial co-occurrence relationships, suggesting that community assembly was dominated by habitat filtering in sediments. Notably, communities colonizing more extreme conditions tended to be highly competitive, which was typically accompanied with increased network complexity but decreased stability of the microbiome. Finally, our results demonstrated that heterotrophic Thermoplasmatota associated with ferric iron and sulfate reduction contributed most to the elevated levels of competition. Our study shed light on the cooperative and competitive metabolisms of microbiome in the hazardous AMD sediments, which may provide preliminary clues for the AMD bioremediation in the future.
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Affiliation(s)
- Shao-Ming Gao
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Pandeng Wang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Qi Li
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Wen-Sheng Shu
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China
| | - Ling-Yun Tang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Zhi-Liang Lin
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China
| | - Jin-Tian Li
- School of Life Sciences, South China Normal University, Guangzhou 510631, PR China.
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, PR China.
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3
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Deng D, Yang Z, Yang Y, Wan W, Liu W, Xiong X. Metagenomic insights into nitrogen-cycling microbial communities and their relationships with nitrogen removal potential in the Yangtze River. WATER RESEARCH 2024; 265:122229. [PMID: 39154395 DOI: 10.1016/j.watres.2024.122229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 08/01/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024]
Abstract
Nitrogen (N) pollution is a major threat to river ecosystems worldwide. Elucidating the community structure of N-cycling microorganisms in rivers is essential to understanding how ecosystem processes and functions will respond to increasing N inputs. However, previous studies generally focus on limited functional genes through amplicon sequencing or quantitative PCR techniques and cannot cover all N-cycling microorganisms. Here, metagenomic sequencing and genome binning were used to determine N-cycling genes in water, channel sediments, and riparian soils of the Yangtze River, which has been heavily polluted by N. Additionally, the denitrification and anaerobic ammonium oxidation (anammox) rates that reflect N removal potential were measured using 15N isotope pairing technique. Results showed that functional genes involved in organic N metabolism (i.e., organic degradation and synthesis) and nitrate reduction pathways (i.e., dissimilatory and assimilatory nitrate reduction to ammonium and denitrification) were more abundant and diverse than other N-cycling genes. A total of 121 metagenome-assembled genomes (MAGs) were identified to be involved in N-cycling processes, and the key MAGs were mainly taxonomically classified as Alphaproteobacteria and Gammaproteobacteria. The abundance and diversity of most N-cycling genes were higher in soils and sediments than in water, as well as higher in downstream and midstream than in upstream sites. These spatial variations were explained not only by local environment and vegetation but also by geographical and climatic factors. N removal process (i.e., denitrification and anammox) rates were significantly related to the abundance or diversity of several N-cycling genes, and climate and edaphic factors could regulate denitrification and anammox rates directly and indirectly through their effects on functional genes. Overall, these results provide a new avenue for further understanding the biogeographic patterns and environmental drivers of N-cycling microorganisms in rivers from the metagenomic perspective.
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Affiliation(s)
- Danli Deng
- Post Doctoral Research Station of Hydraulic Engineering of Three Gorges University, Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang 443002, China; Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
| | - Zhengjian Yang
- Post Doctoral Research Station of Hydraulic Engineering of Three Gorges University, Hubei Field Observation and Scientific Research Stations for Water Ecosystem in Three Gorges Reservoir, China Three Gorges University, Yichang 443002, China
| | - Yuyi Yang
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China
| | - Wenjie Wan
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China
| | - Wenzhi Liu
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China.
| | - Xiang Xiong
- Hubei Key Laboratory of Wetland Evolution & Ecological Restoration, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, The Chinese Academy of Sciences & Hubei Province, Wuhan 430074, China.
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4
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Zhang D, Liu F, Al MA, Yang Y, Yu H, Li M, Wu K, Niu M, Wang C, He Z, Yan Q. Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 928:172518. [PMID: 38631637 DOI: 10.1016/j.scitotenv.2024.172518] [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: 02/14/2024] [Revised: 04/13/2024] [Accepted: 04/14/2024] [Indexed: 04/19/2024]
Abstract
Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4+, NO2- and SO42, while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.
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Affiliation(s)
- Dandan Zhang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Fei Liu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Mamun Abdullah Al
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Yuchun Yang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Huang Yu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China; School of Resources Environment and Safety Engineering, Key Discipline Laboratory for National Defense for Biotechnology in Uranium Mining and Hydrometallurgy, University of South China, Hengyang 421001, China
| | - Mingyue Li
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Kun Wu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Mingyang Niu
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Cheng Wang
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Zhili He
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China
| | - Qingyun Yan
- School of Environmental Science and Engineering, Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), School of Ecology, Guangdong Provincial Observation and Research Station for Marine Ranching in Lingdingyang Bay, China-ASEAN Belt and Road Joint Laboratory on Mariculture Technology, State Key Laboratory for Biocontrol, Sun Yat-sen University, Guangzhou 510006, China.
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5
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Isokpehi RD, Kim Y, Krejci SE, Trivedi VD. Ecological Trait-Based Digital Categorization of Microbial Genomes for Denitrification Potential. Microorganisms 2024; 12:791. [PMID: 38674735 PMCID: PMC11052009 DOI: 10.3390/microorganisms12040791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
Microorganisms encode proteins that function in the transformations of useful and harmful nitrogenous compounds in the global nitrogen cycle. The major transformations in the nitrogen cycle are nitrogen fixation, nitrification, denitrification, anaerobic ammonium oxidation, and ammonification. The focus of this report is the complex biogeochemical process of denitrification, which, in the complete form, consists of a series of four enzyme-catalyzed reduction reactions that transforms nitrate to nitrogen gas. Denitrification is a microbial strain-level ecological trait (characteristic), and denitrification potential (functional performance) can be inferred from trait rules that rely on the presence or absence of genes for denitrifying enzymes in microbial genomes. Despite the global significance of denitrification and associated large-scale genomic and scholarly data sources, there is lack of datasets and interactive computational tools for investigating microbial genomes according to denitrification trait rules. Therefore, our goal is to categorize archaeal and bacterial genomes by denitrification potential based on denitrification traits defined by rules of enzyme involvement in the denitrification reduction steps. We report the integration of datasets on genome, taxonomic lineage, ecosystem, and denitrifying enzymes to provide data investigations context for the denitrification potential of microbial strains. We constructed an ecosystem and taxonomic annotated denitrification potential dataset of 62,624 microbial genomes (866 archaea and 61,758 bacteria) that encode at least one of the twelve denitrifying enzymes in the four-step canonical denitrification pathway. Our four-digit binary-coding scheme categorized the microbial genomes to one of sixteen denitrification traits including complete denitrification traits assigned to 3280 genomes from 260 bacteria genera. The bacterial strains with complete denitrification potential pattern included Arcobacteraceae strains isolated or detected in diverse ecosystems including aquatic, human, plant, and Mollusca (shellfish). The dataset on microbial denitrification potential and associated interactive data investigations tools can serve as research resources for understanding the biochemical, molecular, and physiological aspects of microbial denitrification, among others. The microbial denitrification data resources produced in our research can also be useful for identifying microbial strains for synthetic denitrifying communities.
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Affiliation(s)
| | - Yungkul Kim
- Oyster Microbiome Project, College of Science, Engineering and Mathematics, Bethune-Cookman University, Daytona Beach, FL 32114, USA; (S.E.K.); (V.D.T.)
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6
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Pi HW, Lin JJ, Chen CA, Wang PH, Chiang YR, Huang CC, Young CC, Li WH. Origin and evolution of nitrogen fixation in prokaryotes. Mol Biol Evol 2022; 39:6673025. [PMID: 35993177 PMCID: PMC9447857 DOI: 10.1093/molbev/msac181] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
The origin of nitrogen fixation is an important issue in evolutionary biology. While nitrogen is required by all living organisms, only a small fraction of bacteria and archaea can fix nitrogen. The prevailing view is that nitrogen fixation first evolved in archaea and was later transferred to bacteria. However, nitrogen-fixing (Nif) bacteria are far larger in number and far more diverse in ecological niches than Nif archaea. We, therefore, propose the bacteria-first hypothesis, which postulates that nitrogen fixation first evolved in bacteria and was later transferred to archaea. As >30,000 prokaryotic genomes have been sequenced, we conduct an in-depth comparison of the two hypotheses. We first identify the six genes involved in nitrogen fixation in all sequenced prokaryotic genomes and then reconstruct phylogenetic trees using the six Nif proteins individually or in combination. In each of these trees, the earliest lineages are bacterial Nif protein sequences and in the oldest clade (group) the archaeal sequences are all nested inside bacterial sequences, suggesting that the Nif proteins first evolved in bacteria. The bacteria-first hypothesis is further supported by the observation that the majority of Nif archaea carry the major bacterial Mo (molybdenum) transporter (ModABC) rather than the archaeal Mo transporter (WtpABC). Moreover, in our phylogeny of all available ModA and WtpA protein sequences, the earliest lineages are bacterial sequences while archaeal sequences are nested inside bacterial sequences. Furthermore, the bacteria-first hypothesis is supported by available isotopic data. In conclusion, our study strongly supports the bacteria-first hypothesis.
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Affiliation(s)
- Hong Wei Pi
- Ph.D. Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan.,Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Jinn Jy Lin
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chi An Chen
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Genome and Systems Biology Degree Program, Academia Sinica and National Taiwan University, Taipei 10617, Taiwan
| | - Po Hsiang Wang
- Graduate Institute of Environmental Engineering, National Central University, Taoyuan, Taiwan 32001.,Earth-Life Science Institute, Tokyo Institute of Technology, Tokyo, Japan 145-0061
| | - Yin Ru Chiang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529
| | - Chieh Chen Huang
- Department of Life Sciences, National Chung Hsing University, Taichung, Taiwan 402
| | - Chiu Chung Young
- Department of Soil and Environmental Sciences, College of Agriculture and Natural Resources, National Chung Hsing University, Taichung, Taiwan 402
| | - Wen Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan 11529.,Department of Ecology and Evolution, University of Chicago, Chicago 60637, USA
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Mosley OE, Gios E, Close M, Weaver L, Daughney C, Handley KM. Nitrogen cycling and microbial cooperation in the terrestrial subsurface. THE ISME JOURNAL 2022; 16:2561-2573. [PMID: 35941171 PMCID: PMC9562985 DOI: 10.1038/s41396-022-01300-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 07/19/2022] [Accepted: 07/22/2022] [Indexed: 11/25/2022]
Abstract
The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.
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Genomic Features and Pervasive Negative Selection in Rhodanobacter Strains Isolated from Nitrate and Heavy Metal Contaminated Aquifer. Microbiol Spectr 2022; 10:e0259121. [PMID: 35107332 PMCID: PMC8809349 DOI: 10.1128/spectrum.02591-21] [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] [Indexed: 12/31/2022] Open
Abstract
Rhodanobacter species dominate in the Oak Ridge Reservation (ORR) subsurface environments contaminated with acids, nitrate, metal radionuclides, and other heavy metals. To uncover the genomic features underlying adaptations to these mixed-waste environments and to guide genetic tool development, we sequenced the whole genomes of eight Rhodanobacter strains isolated from the ORR site. The genome sizes ranged from 3.9 to 4.2 Mb harboring 3,695 to 4,035 protein-coding genes and GC contents approximately 67%. Seven strains were classified as R. denitrificans and one strain, FW510-R12, as R. thiooxydans based on full length 16S rRNA sequences. According to gene annotation, the top two Cluster of Orthologous Groups (COGs) with high pan-genome expansion rates (Pan/Core gene ratio) were “replication, recombination and repair” and “defense mechanisms.” The denitrifying genes had high DNA homologies except the predicted protein structure variances in NosZ. In contrast, heavy metal resistance genes were diverse with between 7 to 34% of them were located in genomic islands, and these results suggested origins from horizontal gene transfer. Analysis of the methylation patterns in four strains revealed the unique 5mC methylation motifs. Most orthologs (78%) had ratios of nonsynonymous to synonymous substitutions (dN/dS) less than one when compared to the type strain 2APBS1, suggesting the prevalence of negative selection. Overall, the results provide evidence for the important roles of horizontal gene transfer and negative selection in genomic adaptation at the contaminated field site. The complex restriction-modification system genes and the unique methylation motifs in Rhodanobacter strains suggest the potential recalcitrance to genetic manipulation. IMPORTANCE Despite the dominance of Rhodanobacter species in the subsurface of the contaminated Oak Ridge Reservation (ORR) site, very little is known about the mechanisms underlying their adaptions to the various stressors present at ORR. Recently, multiple Rhodanobacter strains have been isolated from the ORR groundwater samples from several wells with varying geochemical properties. Using Illumina, PacBio, and Oxford Nanopore sequencing platforms, we obtained the whole genome sequences of eight Rhodanobacter strains. Comparison of the whole genomes demonstrated the genetic diversity, and analysis of the long nanopore reads revealed the heterogeneity of methylation patterns in strains isolated from the same well. Although all strains contained a complete set of denitrifying genes, the predicted tertiary structures of NosZ differed. The sequence comparison results demonstrate the important roles of horizontal gene transfer and negative selection in adaptation. In addition, these strains may be recalcitrant to genetic manipulation due to the complex restriction-modification systems and methylations.
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Wang P, Li J, Luo X, Ahmad M, Duan L, Yin L, Fang B, Li S, Yang Y, Jiang L, Li W. Biogeographical distributions of nitrogen‐cycling functional genes in a subtropical estuary. Funct Ecol 2021. [DOI: 10.1111/1365-2435.13949] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Pandeng Wang
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Jia‐Ling Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Xiao‐Qing Luo
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Manzoor Ahmad
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Li Duan
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Ling‐Zi Yin
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Bao‐Zhu Fang
- State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Urumqi PR China
| | - Shan‐Hui Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Yuchun Yang
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
| | - Lin Jiang
- School of Biological Sciences Georgia Institute of Technology Atlanta GA USA
| | - Wen‐Jun Li
- State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai) School of Ecology & School of Life Sciences Sun Yat‐Sen University Guangzhou PR China
- State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and Geography Chinese Academy of Sciences Urumqi PR China
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10
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Toxic Effect of Ammonium Nitrogen on the Nitrification Process and Acclimatisation of Nitrifying Bacteria to High Concentrations of NH4-N in Wastewater. ENERGIES 2021. [DOI: 10.3390/en14175329] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The aim of the conducted research was to assess the effectiveness of the nitrification process, at different concentrations of ammonium nitrogen, in biologically treated wastewater in one of the largest municipal and industrial wastewater treatment plants in Poland. The studies also attempted to acclimate nitrifying bacteria to the limited concentration of ammonium nitrogen and determined the efficiency of nitrification under the influence of acclimated activated sludge in the biological wastewater treatment system. The obtained results indicate that the concentration of ammonium nitrogen above 60.00 mg·dm−3 inhibits nitrification, even after increasing the biomass of nitrifiers. The increase in the efficiency of the nitrification process in the tested system can be obtained by using the activated sludge inoculated with nitrifiers. For this purpose, nitrifiers should be preacclimated, at least for a period of time, allowing them to colonize the activated sludge. The acclimated activated sludge allows reducing the amount of ammonium nitrogen in treated sewage by approx. 35.0%. The process of stable nitrification in the biological treatment system was observed nine days after introducing the acclimated activated sludge into the aeration chamber.
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You Y, Aho K, Lohse KA, Schwabedissen SG, Ledbetter RN, Magnuson TS. Biological Soil Crust Bacterial Communities Vary Along Climatic and Shrub Cover Gradients Within a Sagebrush Steppe Ecosystem. Front Microbiol 2021; 12:569791. [PMID: 34025590 PMCID: PMC8134670 DOI: 10.3389/fmicb.2021.569791] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 04/13/2021] [Indexed: 11/19/2022] Open
Abstract
Numerous studies have examined bacterial communities in biological soil crusts (BSCs) associated with warm arid to semiarid ecosystems. Few, however, have examined bacterial communities in BSCs associated with cold steppe ecosystems, which often span a wide range of climate conditions and are sensitive to trends predicted by relevant climate models. Here, we utilized Illumina sequencing to examine BSC bacterial communities with respect to climatic gradients (elevation), land management practices (grazing vs. non-grazing), and shrub/intershrub patches in a cold sagebrush steppe ecosystem in southwestern Idaho, United States. Particular attention was paid to shifts in bacterial community structure and composition. BSC bacterial communities, including keystone N-fixing taxa, shifted dramatically with both elevation and shrub-canopy microclimates within elevational zones. BSC cover and BSC cyanobacteria abundance were much higher at lower elevation (warmer and drier) sites and in intershrub areas. Shrub-understory BSCs were significantly associated with several non-cyanobacteria diazotrophic genera, including Mesorhizobium and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium. High elevation (wetter and colder) sites had distinct, highly diverse, but low-cover BSC communities that were significantly indicated by non-cyanobacterial diazotrophic taxa including families in the order Rhizobiales and the family Frankiaceae. Abiotic soil characteristics, especially pH and ammonium, varied with both elevation and shrub/intershrub level, and were strongly associated with BSC community composition. Functional inference using the PICRUSt pipeline identified shifts in putative N-fixing taxa with respect to both the elevational gradient and the presence/absence of shrub canopy cover. These results add to current understanding of biocrust microbial ecology in cold steppe, serving as a baseline for future mechanistic research.
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Lv J, Niu Y, Yuan R, Wang S. Different Responses of Bacterial and Archaeal Communities in River Sediments to Water Diversion and Seasonal Changes. Microorganisms 2021; 9:microorganisms9040782. [PMID: 33917984 PMCID: PMC8068392 DOI: 10.3390/microorganisms9040782] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/06/2021] [Accepted: 04/07/2021] [Indexed: 11/16/2022] Open
Abstract
In recent years, different responses of archaea and bacteria to environmental changes have attracted increasing scientific interest. In the mid-latitude region, Fen River receives water transferred from the Yellow River, electrical conductivity (EC), concentrations of Cl- and Na+ in water, total phosphorus (TP), and Olsen phosphorus (OP) in sediments were significantly affected by water transfer. Meanwhile, temperature and oxidation-reduction potential (ORP) of water showed significant seasonal variations. Based on 16S rRNA high-throughput sequencing technology, the composition of bacteria and archaea in sediments was determined in winter and summer, respectively. Results showed that the dominance of bacterial core flora decreased and that of archaeal core flora increased after water diversion. The abundance and diversity of bacterial communities in river sediments were more sensitive to anthropogenic and naturally induced environmental changes than that of archaeal communities. Bacterial communities showed greater resistance than archaeal communities under long-term external disturbances, such as seasonal changes, because of rich species composition and complex community structure. Archaea were more stable than bacteria, especially under short-term drastic environmental disturbances, such as water transfer, due to their insensitivity to environmental changes. These results have important implications for understanding the responses of bacterial and archaeal communities to environmental changes in river ecosystems affected by water diversion.
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Affiliation(s)
- Jiali Lv
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China;
- Sino-Danish College of University of Chinese Academy of Sciences, Beijing 101408, China
| | - Yangdan Niu
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
| | - Ruiqiang Yuan
- School of Environment and Natural Resources, Shanxi University, Taiyuan 030006, China; (J.L.); (Y.N.)
- Correspondence:
| | - Shiqin Wang
- Key Laboratory of Agricultural Water Resources Research, Innovation Academy for Seed Design, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China;
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Marzocchi U, Bonaglia S, Zaiko A, Quero GM, Vybernaite-Lubiene I, Politi T, Samuiloviene A, Zilius M, Bartoli M, Cardini U. Zebra Mussel Holobionts Fix and Recycle Nitrogen in Lagoon Sediments. Front Microbiol 2021; 11:610269. [PMID: 33542710 PMCID: PMC7851879 DOI: 10.3389/fmicb.2020.610269] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/29/2020] [Indexed: 01/04/2023] Open
Abstract
Bivalves are ubiquitous filter-feeders able to alter ecosystems functions. Their impact on nitrogen (N) cycling is commonly related to their filter-feeding activity, biodeposition, and excretion. A so far understudied impact is linked to the metabolism of the associated microbiome that together with the host constitute the mussel's holobiont. Here we investigated how colonies of the invasive zebra mussel (Dreissena polymorpha) alter benthic N cycling in the shallow water sediment of the largest European lagoon (the Curonian Lagoon). A set of incubations was conducted to quantify the holobiont's impact and to quantitatively compare it with the indirect influence of the mussel on sedimentary N transformations. Zebra mussels primarily enhanced the recycling of N to the water column by releasing mineralized algal biomass in the form of ammonium and by stimulating dissimilatory nitrate reduction to ammonium (DNRA). Notably, however, not only denitrification and DNRA, but also dinitrogen (N2) fixation was measured in association with the holobiont. The diazotrophic community of the holobiont diverged substantially from that of the water column, suggesting a unique niche for N2 fixation associated with the mussels. At the densities reported in the lagoon, mussel-associated N2 fixation may account for a substantial (and so far, overlooked) source of bioavailable N. Our findings contribute to improve our understanding on the ecosystem-level impact of zebra mussel, and potentially, of its ability to adapt to and colonize oligotrophic environments.
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Affiliation(s)
- Ugo Marzocchi
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Center for Water Technology (WATEC), Department of Biology, Aarhus University, Aarhus, Denmark
| | - Stefano Bonaglia
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
- Nordcee, Department of Biology, University of Southern Denmark, Odense, Denmark
- Department of Marine Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Anastasija Zaiko
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Coastal and Freshwater Group, Cawthron Institute, Nelson, New Zealand
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
| | - Grazia M. Quero
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Institute for Biological Resources and Marine Biotechnologies, National Research Council of Italy, Ancona, Italy
| | | | - Tobia Politi
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
| | | | - Mindaugas Zilius
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Marco Bartoli
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
- Department of Chemistry, Life science and Environmental Sustainability, Parma University, Parma, Italy
| | - Ulisse Cardini
- Integrative Marine Ecology Department, Stazione Zoologica Anton Dohrn, National Institute of Marine Biology, Ecology and Biotechnology, Naples, Italy
- Marine Research Institute, Klaipėda University, Klaipėda, Lithuania
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Cox AH, Wigginton SK, Amador JA. Structure of greenhouse gas-consuming microbial communities in surface soils of a nitrogen-removing experimental drainfield. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 739:140362. [PMID: 32758972 DOI: 10.1016/j.scitotenv.2020.140362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 05/13/2020] [Accepted: 06/17/2020] [Indexed: 06/11/2023]
Abstract
Septic systems represent a source of greenhouse gases generated by microbial processes as wastewater constituents are degraded. Both aerobic and anerobic wastewater transformation processes can generate nitrous oxide and methane, both of which are potent greenhouse gases (GHGs). To understand how microbial communities in the surface soils above shallow drainfields contribute to methane and nitrous oxide consumption, we measured greenhouse gas surface flux and below-ground concentrations and compared them to the microbial communities present using functional genes pmoA and nosZ. These genes encode portions of particulate methane monooxygenase and nitrous oxide reductase, respectively, serving as a potential sink for the respective greenhouse gases. We assessed the surface soils above three drainfields served by a single household: an experimental layered passive N-reducing drainfield, a control conventional drainfield, and a reserve drainfield not in use but otherwise identical to the control. We found that neither GHG flux, below-ground concentration or soil properties varied among drainfield types, nor did methane oxidizing and nitrous oxide reducing communities vary by drainfield type. We found differences in pmoA and nosZ communities based on depth from the soil surface, and differences in nosZ communities based on whether the sample came from the rhizosphere or surrounding bulk soils. Type I methanotrophs (Gammaproteobacteria) were more abundant in the upper and middle portions of the soil above the drainfield. In general, we found no relationship in community composition for either gene based on GHG flux or below-ground concentration or soil properties (bulk density, organic matter, above-ground biomass). This is the first study to assess these communities in the surface soils above an experimental working drainfield, and more research is needed to understand the dynamics of greenhouse gas production and consumption in these systems.
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Affiliation(s)
- Alissa H Cox
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
| | - Sara K Wigginton
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
| | - José A Amador
- Department of Natural Resources Science, University of Rhode Island, 1 Greenhouse Rd, Kingston, RI 02881, USA.
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Nitrifying and Denitrifying Microbial Communities in Centralized and Decentralized Biological Nitrogen Removing Wastewater Treatment Systems. WATER 2020. [DOI: 10.3390/w12061688] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Biological nitrogen removal (BNR) in centralized and decentralized wastewater treatment systems is assumed to be driven by the same microbial processes and to have communities with a similar composition and structure. There is, however, little information to support these assumptions, which may impact the effectiveness of decentralized systems. We used high-throughput sequencing to compare the structure and composition of the nitrifying and denitrifying bacterial communities of nine onsite wastewater treatment systems (OWTS) and one wastewater treatment plant (WTP) by targeting the genes coding for ammonia monooxygenase (amoA) and nitrous oxide reductase (nosZ). The amoA diversity was similar between the WTP and OWTS, but nosZ diversity was generally higher for the WTP. Beta diversity analyses showed the WTP and OWTS promoted distinct amoA and nosZ communities, although there is a core group of N-transforming bacteria common across scales of BNR treatment. Our results suggest that advanced N-removal OWTS have microbial communities that are sufficiently distinct from those of WTP with BNR, which may warrant different management approaches.
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Garcia MO, Templer PH, Sorensen PO, Sanders-DeMott R, Groffman PM, Bhatnagar JM. Soil Microbes Trade-Off Biogeochemical Cycling for Stress Tolerance Traits in Response to Year-Round Climate Change. Front Microbiol 2020; 11:616. [PMID: 32477275 PMCID: PMC7238748 DOI: 10.3389/fmicb.2020.00616] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 03/19/2020] [Indexed: 01/16/2023] Open
Abstract
Winter air temperatures are rising faster than summer air temperatures in high-latitude forests, increasing the frequency of soil freeze/thaw events in winter. To determine how climate warming and soil freeze/thaw cycles affect soil microbial communities and the ecosystem processes they drive, we leveraged the Climate Change across Seasons Experiment (CCASE) at the Hubbard Brook Experimental Forest in the northeastern United States, where replicate field plots receive one of three climate treatments: warming (+5°C above ambient in the growing season), warming in the growing season + winter freeze/thaw cycles (+5°C above ambient +4 freeze/thaw cycles during winter), and no treatment. Soil samples were taken from plots at six time points throughout the growing season and subjected to amplicon (rDNA) and metagenome sequencing. We found that soil fungal and bacterial community composition were affected by changes in soil temperature, where the taxonomic composition of microbial communities shifted more with the combination of growing-season warming and increased frequency of soil freeze/thaw cycles in winter than with warming alone. Warming increased the relative abundance of brown rot fungi and plant pathogens but decreased that of arbuscular mycorrhizal fungi, all of which recovered under combined growing-season warming and soil freeze/thaw cycles in winter. The abundance of animal parasites increased significantly under combined warming and freeze/thaw cycles. We also found that warming and soil freeze/thaw cycles suppressed bacterial taxa with the genetic potential for carbon (i.e., cellulose) decomposition and soil nitrogen cycling, such as N fixation and the final steps of denitrification. These new soil communities had higher genetic capacity for stress tolerance and lower genetic capacity to grow or reproduce, relative to the communities exposed to warming in the growing season alone. Our observations suggest that initial suppression of biogeochemical cycling with year-round climate change may be linked to the emergence of taxa that trade-off growth for stress tolerance traits.
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Affiliation(s)
- Maria O. Garcia
- Department of Biology, Boston University, Boston, MA, United States
| | | | - Patrick O. Sorensen
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Rebecca Sanders-DeMott
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter M. Groffman
- Advanced Science Research Center at the Graduate Center, City University of New York, New York, NY, United States
- Cary Institute of Ecosystem Studies, Millbrook, NY, United States
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Liu K, Cai M, Hu C, Sun X, Cheng Q, Jia W, Yang T, Nie M, Zhao X. Selenium (Se) reduces Sclerotinia stem rot disease incidence of oilseed rape by increasing plant Se concentration and shifting soil microbial community and functional profiles. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:113051. [PMID: 31450117 DOI: 10.1016/j.envpol.2019.113051] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Revised: 07/27/2019] [Accepted: 08/11/2019] [Indexed: 05/21/2023]
Abstract
Sclerotinia stem rot (SSR), a soil-borne plant disease, cause the yield loss of oilseed rape. Selenium (Se), a beneficial element of plant, improves plant resistance to pathogens, and regulates microbial communities in soil. Soil microbial communities has been identified to play an important role in plant health. We studied whether the changes in soil microbiome under influence of Se associated with oilseed rape health. SSR disease incidence of oilseed rape and soil biochemical properties were investigated in Enshi district, "The World Capital of Selenium", and soil bacterial and fungal communities were analyzed by 16S rRNA and ITS sequencing, respectively. Results showed that Se had a strong effect on SSR incidence, and disease incidence inversely related with plant Se concentration. Besides, soil Se enhanced the microbiome diversities and the relative abundance of PGPR (plant growth promoting rhizobacteria), such as Bryobacter, Nitrospirae, Rhizobiales, Xanthobacteraceae, Nitrosomonadaceae and Basidiomycota. Furthermore, Soil Se decreased the relative abundance of pathogenic fungi, such as Olpidium, Armillaria, Coniosporium, Microbotryomycetes and Chytridiomycetes. Additionally, Se increased nitrogen metabolism, carbohydrate metabolism and cell processes related functional profiles in soil. The enrichment of Se in plants and improvement of soil microbial community were related to increased plant resistance to pathogen infection. These findings suggested that Se has potential to be developed as an ecological fungicide for biological control of SSR.
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Affiliation(s)
- Kang Liu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Miaomiao Cai
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Chengxiao Hu
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xuecheng Sun
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Qin Cheng
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei Jia
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Tao Yang
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Min Nie
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaohu Zhao
- Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs/Hubei Provincial Engineering Laboratory for New Fertilizers/Research Center of Trace Elements, College of Resources and Environment, Huazhong Agricultural University, Wuhan 430070, China.
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18
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Svatos KBW, Abbott LK. Dairy soil bacterial responses to nitrogen application in simulated Italian ryegrass and white clover pasture. J Dairy Sci 2019; 102:9495-9504. [PMID: 31351712 DOI: 10.3168/jds.2018-16107] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 06/01/2019] [Indexed: 11/19/2022]
Abstract
Through clearing and use of fertilizer and legumes, areas of southwestern Australia's unique coastal sand plains can support relatively low-cost dairies. However, the ancient, highly weathered nature of the soils in this region makes the dairies susceptible to a range of threats, including nutrient leaching and erosion. Despite this, Western Australian dairy cows typically produce up to 5,500 L of milk per head annually supported by inorganic nitrogen (N) fertilizer (commonly 50:50 urea and ammonium sulfate) at rates up to <320 kg of N/ha per year. Where hotspots exist (up to 2,000 kg of N/ha per year), total N exceeds pasture requirements. We investigated plant and soil bacteria responses to N fertilizer rates consistent with Australian legislated production practices on dairy farms for pure and mixed swards of white clover (Trifolium repens) and Italian ryegrass (Lolium multiflorum) in a long-term pasture experiment in controlled glasshouse conditions. Although the soil bacterial community structure at phylum level was similar for white clover and Italian ryegrass, relative abundances of specific subgroups of bacteria differed among plant species according to the N fertilizer regimen. Marked increases in relative abundance of some bacterial phyla and subphyla indicated potential inhibition of N cycling, especially for N hotspots in soil. Ammonium concentration in soil was less correlated with dominance of some N-cycling bacterial phyla than was nitrate concentration. Changes in bacterial community structure related to altered nutrient cycling highlight the potential for considering this area of research in policy assessment frameworks related to nutrient loads in dairy soils, especially for N.
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Affiliation(s)
- Karl B W Svatos
- UWA School of Agriculture and Environment, The University of Western Australia, Perth 6009, Western Australia, Australia; School of Veterinary and Life Sciences, Murdoch University, Murdoch 6150, Western Australia, Australia; Agriculture and Food Division, Department of Primary Industries and Regional Development, South Perth 6151, Western Australia, Australia.
| | - Lynette K Abbott
- UWA School of Agriculture and Environment, The University of Western Australia, Perth 6009, Western Australia, Australia
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Isobe K, Allison SD, Khalili B, Martiny AC, Martiny JBH. Phylogenetic conservation of bacterial responses to soil nitrogen addition across continents. Nat Commun 2019; 10:2499. [PMID: 31175309 PMCID: PMC6555827 DOI: 10.1038/s41467-019-10390-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 05/03/2019] [Indexed: 11/24/2022] Open
Abstract
Soil microbial communities are intricately linked to ecosystem functioning such as nutrient cycling; therefore, a predictive understanding of how these communities respond to environmental changes is of great interest. Here, we test whether phylogenetic information can predict the response of bacterial taxa to nitrogen (N) addition. We analyze the composition of soil bacterial communities in 13 field experiments across 5 continents and find that the N response of bacteria is phylogenetically conserved at each location. Remarkably, the phylogenetic pattern of N responses is similar when merging data across locations. Thus, we can identify bacterial clades - the size of which are highly variable across the bacterial tree - that respond consistently to N addition across locations. Our findings suggest that a phylogenetic approach may be useful in predicting shifts in microbial community composition in the face of other environmental changes.
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Affiliation(s)
- Kazuo Isobe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, 113-8657, Japan.
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
| | - Banafshe Khalili
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA
- Department of Earth System Science, University of California, Irvine, CA, 92697, USA
| | - Jennifer B H Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, 92697, USA.
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