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Bernthal FR, Armstrong JD, Nislow KH, Metcalfe NB. Nutrient limitation in Atlantic salmon rivers and streams: Causes, consequences, and management strategies. AQUATIC CONSERVATION : MARINE AND FRESHWATER ECOSYSTEMS 2022; 32:1073-1091. [PMID: 35915662 PMCID: PMC9314074 DOI: 10.1002/aqc.3811] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 02/17/2022] [Accepted: 03/06/2022] [Indexed: 06/16/2023]
Abstract
Freshwater catchments can experience nutrient deficits that result in reduced primary and secondary productivity. The most commonly limiting nutrients are nitrogen and phosphorus, either separately or together. This review considers the impact of increasing nutrient limitation in temperate basin stream and river systems, focusing on upland areas that currently or previously supported wild Atlantic salmon (Salmo salar) populations.Anthropogenic changes to land use and increases in river barriers have altered upland nutrient dynamics, with particular impacts on salmon and other migratory fish species which may be net importers of nutrients to upland streams. Declining salmon populations may further reduce nutrient sources, reducing ecosystem and fisheries productivity below desired levels.Experimental manipulations of nutrient levels have examined the impacts of this cultural oligotrophication. There is evidence that growth and biomass of juvenile salmon can be increased via appropriate additions of nutrients, offering potential as a conservation tool. However, further research is required to understand the long-term effects of these additions on salmon populations and stream ecosystems, and to assess the vulnerability of downstream habitats to eutrophication as a result.Although purposeful nutrient addition with the aim of enhancing and conserving salmonid populations may be justified in some cases, it should be undertaken in an adaptive management framework. In addition, nutrient addition should be linked to nutrient retention and processing, and integrated into large-scale habitat restoration and recovery efforts.Both the scientific and the management community should recognize that the ecological costs and benefits associated with adding nutrients to salmon streams may change in a non-stationary world.
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Affiliation(s)
- Fionn R. Bernthal
- Institute of Biodiversity Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
| | - John D. Armstrong
- Marine Scotland – ScienceFreshwater Fisheries LaboratoryFaskallyPitlochryUK
| | - Keith H. Nislow
- USDA Forest Service Northern Research StationAmherstMassachusettsUSA
| | - Neil B. Metcalfe
- Institute of Biodiversity Animal Health and Comparative MedicineUniversity of GlasgowGlasgowUK
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Xie Y, Zhu L, Lyu G, Lu L, Ma J, Ma J. Persistence of E. coli O157:H7 in urban recreational waters from Spring and Autumn: a comparison analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:39088-39101. [PMID: 35098467 DOI: 10.1007/s11356-021-18407-0] [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: 08/25/2021] [Accepted: 12/26/2021] [Indexed: 06/14/2023]
Abstract
People might get infected by pathogens found in urban recreational waters during water-contact activities, such as swimming, boating, bathing, and yachting. However, the persistence of pathogenic bacteria in those waters was not well documented. In this study, persistence of E. coli O157:H7 (EcO157) in 48 water samples (24 Spring samples and 24 Autumn samples) from the 3 urban recreational waters was investigated. Multivariate statistical analysis was performed to correlate survival data with water physicochemical properties and bacterial communities. Our data showed that EcO157 survived longer in Spring samples than in Autumn samples regardless of the lakes. Results revealed that recreational water physicochemical properties and bacterial community in Spring samples were different from those in Autumn samples. Mantel and Partial Mantel tests, as well as co-occurrence network analysis illustrated that EC salinity, TOC, and bacterial community were correlated with survival time (ttd) (p < 0.05). Variation partition analysis (VPA) indicated that bacterial community, EC, TOC, and TN explained about 64.81% of overall ttd variation in Spring samples, and bacterial community, EC, pH, and TP accounted for about 56.59% of overall ttd variation in Autumn samples. Structural equation model (SEM) illustrated that EC indirectly positively affected ttd through bacterial community. The correlation between bacterial community and ttd was negative in Spring samples and positive in Autumn samples. TN appeared a direct positive effect on ttd in Spring samples. TP displayed a direct negative effect on ttd in Autumn samples. Our results concluded that there was seasonal variation in environmental factors that directly or indirectly affected the survival of EcO157 in urban recreational waters.
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Affiliation(s)
- Yuang Xie
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
- Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, 130021, China
| | - Liyue Zhu
- Songliao River Basin Ecology and Environment Administration, Ministry of Ecology and Environment, Changchun, 130021, China
| | - Guangze Lyu
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
| | - Lu Lu
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
| | - Jinhua Ma
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China
| | - Jincai Ma
- Key Laboratory of Groundwater Resources and Environment, Ministry of Education, Jilin University, Changchun, 130021, China.
- Jilin Provincial Key Laboratory of Water Resources and Environment, College of New Energy and Environment, Jilin University, Changchun, 130021, China.
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Rodríguez‐Cardona BM, Wymore AS, Argerich A, Barnes RT, Bernal S, Brookshire ENJ, Coble AA, Dodds WK, Fazekas HM, Helton AM, Johnes PJ, Johnson SL, Jones JB, Kaushal SS, Kortelainen P, López‐Lloreda C, Spencer RGM, McDowell WH. Shifting stoichiometry: Long-term trends in stream-dissolved organic matter reveal altered C:N ratios due to history of atmospheric acid deposition. GLOBAL CHANGE BIOLOGY 2022; 28:98-114. [PMID: 34706120 PMCID: PMC9297910 DOI: 10.1111/gcb.15965] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 09/26/2021] [Indexed: 05/15/2023]
Abstract
Dissolved organic carbon (DOC) and nitrogen (DON) are important energy and nutrient sources for aquatic ecosystems. In many northern temperate, freshwater systems DOC has increased in the past 50 years. Less is known about how changes in DOC may vary across latitudes, and whether changes in DON track those of DOC. Here, we present long-term DOC and DON data from 74 streams distributed across seven sites in biomes ranging from the tropics to northern boreal forests with varying histories of atmospheric acid deposition. For each stream, we examined the temporal trends of DOC and DON concentrations and DOC:DON molar ratios. While some sites displayed consistent positive or negative trends in stream DOC and DON concentrations, changes in direction or magnitude were inconsistent at regional or local scales. DON trends did not always track those of DOC, though DOC:DON ratios increased over time for ~30% of streams. Our results indicate that the dissolved organic matter (DOM) pool is experiencing fundamental changes due to the recovery from atmospheric acid deposition. Changes in DOC:DON stoichiometry point to a shifting energy-nutrient balance in many aquatic ecosystems. Sustained changes in the character of DOM can have major implications for stream metabolism, biogeochemical processes, food webs, and drinking water quality (including disinfection by-products). Understanding regional and global variation in DOC and DON concentrations is important for developing realistic models and watershed management protocols to effectively target mitigation efforts aimed at bringing DOM flux and nutrient enrichment under control.
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Affiliation(s)
- Bianca M. Rodríguez‐Cardona
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
- Département des sciences biologiquesUniversité du Québec à MontréalMontréalQuébecCanada
| | - Adam S. Wymore
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
| | - Alba Argerich
- School of Natural ResourcesUniversity of MissouriColumbiaMissouriUSA
| | - Rebecca T. Barnes
- Environmental Studies ProgramColorado CollegeColorado SpringsColoradoUSA
| | - Susana Bernal
- Centre d’Estudis Avançats de Blanes (CEAB‐CSIC)BlanesSpain
| | - E. N. Jack Brookshire
- Department of Land Resources and Environmental SciencesMontana State UniversityBozemanMontanaUSA
| | - Ashley A. Coble
- National Council for Air and Stream Improvement, Inc.CorvallisOregonUSA
| | - Walter K. Dodds
- Division of BiologyKansas State UniversityManhattanKansasUSA
| | - Hannah M. Fazekas
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
| | - Ashley M. Helton
- Department of Natural Resources and the Environment, and the Center for Environmental Sciences and EngineeringUniversity of ConnecticutStorrsConnecticutUSA
| | - Penny J. Johnes
- School of Geographical SciencesUniversity of BristolBristolUK
| | - Sherri L. Johnson
- USDA Forest ServicePacific Northwest Research StationCorvallisOregonUSA
| | - Jeremy B. Jones
- Institute of Arctic Biology & Department of Biology and WildlifeUniversity of Alaska FairbanksFairbanksAlaskaUSA
| | - Sujay S. Kaushal
- Department of GeologyUniversity of MarylandCollege ParkMarylandUSA
| | | | - Carla López‐Lloreda
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
- Department of Biological SciencesVirginia Polytechnic Institute and State UniversityBlacksburgVirginiaUSA
| | - Robert G. M. Spencer
- Department of Earth, Ocean and Atmospheric SciencesFlorida State UniversityTallahasseeFloridaUSA
| | - William H. McDowell
- Department of Natural Resources and the EnvironmentUniversity of New HampshireDurhamNew HampshireUSA
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Ghuneim LAJ, Distaso MA, Chernikova TN, Bargiela R, Lunev EA, Korzhenkov AA, Toshchakov SV, Rojo D, Barbas C, Ferrer M, Golyshina OV, Golyshin PN, Jones DL. Utilization of low-molecular-weight organic compounds by the filterable fraction of a lotic microbiome. FEMS Microbiol Ecol 2021; 97:fiaa244. [PMID: 33264383 PMCID: PMC7864478 DOI: 10.1093/femsec/fiaa244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/30/2020] [Indexed: 11/14/2022] Open
Abstract
Filterable microorganisms participate in dissolved organic carbon (DOC) cycling in freshwater systems, however their exact functional role remains unknown. We determined the taxonomic identity and community dynamics of prokaryotic microbiomes in the 0.22 µm-filtered fraction and unfiltered freshwater from the Conwy River (North Wales, UK) in microcosms and, using targeted metabolomics and 14C-labelling, examined their role in the utilization of amino acids, organic acids and sugars spiked at environmentally-relevant (nanomolar) concentrations. To identify changes in community structure, we used 16S rRNA amplicon and shotgun sequencing. Unlike the unfiltered water samples where the consumption of DOC was rapid, the filtered fraction showed a 3-day lag phase before the consumption started. Analysis of functional categories of clusters of orthologous groups of proteins (COGs) showed that COGs associated with energy production increased in number in both fractions with substrate addition. The filtered fraction utilized low-molecular-weight (LMW) DOC at much slower rates than the whole community. Addition of nanomolar concentrations of LMW DOC did not measurably influence the composition of the microbial community nor the rate of consumption across all substrate types in either fraction. We conclude that due to their low activity, filterable microorganisms play a minor role in LMW DOC processing within a short residence time of lotic freshwater systems.
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Affiliation(s)
- Lydia-Ann J Ghuneim
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Marco A Distaso
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Tatyana N Chernikova
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Rafael Bargiela
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Evgenii A Lunev
- Institute of Living Systems, Immanuel Kant Baltic Federal University, Kaliningrad, Russia
| | - Aleksei A Korzhenkov
- Kurchatov Center for Genome Research, National Research Center “Kurchatov Institute”, Moscow, Russian Federation
| | - Stepan V Toshchakov
- Winogradsky Institute of Microbiology, FRC Biotechnology, Russian Academy of Sciences, Moscow, Russian Federation
| | - David Rojo
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Coral Barbas
- Centro de Metabolómica y Bioanálisis (CEMBIO), Facultad de Farmacia, Universidad CEU San Pablo, Campus Montepríncipe, Madrid, Spain
| | - Manuel Ferrer
- Institute of Catalysis, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Olga V Golyshina
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Peter N Golyshin
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
- Centre for Environmental Biotechnology, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - David L Jones
- School of Natural Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
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Available Dissolved Organic Carbon Alters Uptake and Recycling of Phosphorus and Nitrogen from River Sediments. WATER 2020. [DOI: 10.3390/w12123321] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Concurrent with nutrient pollution, agriculture has significantly impacted the quantity, composition, and bioavailability of catchment-derived dissolved organic carbon (DOC) in stream ecosystems. Based on the stoichiometric theory, we tested the hypothesis that bioavailable DOC will stimulate the heterotrophic uptake of soluble reactive P (SRP) and inorganic nitrogen in stream sediments. In a simplified laboratory column flow-through study, we exposed stream sediments to additions of glucose, nitrate, and phosphate alone and in combination (+C, +NP, +CNP), and calculated gross and net changes in DOC and nutrients via a mass balance approach. Our results show that glucose-C increased nutrient uptake, but also that NP additions resulted in the enhanced consumption of both native and added organic C. The effects of C addition were stronger on N than P uptake, presumably because labile C stimulated both assimilation and denitrification, while part of the P uptake was due to adsorption. Internal cycling affected net nutrient uptake due to losses of dissolved organically-complexed P and N (DOP and DON). Overall, our study shows that increases in the stoichiometric availability of organic carbon can stimulate N and P sequestration in nutrient-polluted stream sediments. Future studies are required to assess the effects of complex organic carbon sources on nutrient uptake in stream sediments under different environmental conditions, and whether these stoichiometric relations are relevant for ecosystem management.
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Li X, Song Y, Bian Y, Gu C, Yang X, Wang F, Jiang X. Insights into the mechanisms underlying efficient Rhizodegradation of PAHs in biochar-amended soil: From microbial communities to soil metabolomics. ENVIRONMENT INTERNATIONAL 2020; 144:105995. [PMID: 32758715 DOI: 10.1016/j.envint.2020.105995] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 06/08/2020] [Accepted: 07/16/2020] [Indexed: 05/15/2023]
Abstract
The combined effects of biochar amendment and the rhizosphere on the soil metabolic microbiome during the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil remain unknown. In this study, we attempted to characterize a PAH degradation network by coupling the direct PAH degradation with soil carbon cycling. From microbial community structure and functions to metabolic pathways, we revealed the modulation strategies by which biochar and the rhizosphere benefited PAH degradation in soil. Firstly, some PAH degraders were enriched by biochar and the rhizosphere, and their combination promoted the cooperation among these PAH degraders. Simultaneously, under the combined effects of biochar and the rhizosphere, the functional genes participating in upstream PAH degradation were greatly upregulated. Secondly, there were strong co-occurrences between soil microbial community members and metabolites, in particular, some PAH degraders and the metabolites, such as PAH degradation products or common carbon resources, were highlighted in the networks. It shows that the overall downstream carbon metabolism of PAH degradation was also greatly upregulated by the combined effects of biochar and plant roots, showing good survival of the soil microbiome and contributing to PAH biodegradation. Taken together, both soil carbon metabolism and direct contaminant biodegradation are likely to be modulated by the combined effects of biochar and plant roots, jointly benefitting to PAH degradation by soil microbiome. Our study is the first to link PAH degradation with native carbon metabolism by coupling sequencing and soil metabolomics technology, providing new insights into a systematic understanding of PAH degradation by indigenous soil microbiome and their networks.
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Affiliation(s)
- Xiaona Li
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Yang Song
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China.
| | - Yongrong Bian
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Chenggang Gu
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xinglun Yang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Fang Wang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Xin Jiang
- CAS Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Nanjing 210008, China; University of the Chinese Academy of Sciences, Beijing 100049, China
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Wang B, Zhong Z, Wang X, Han X, Yu D, Wang C, Song W, Zheng X, Chen C, Zhang Y. Knockout of the OsNAC006 Transcription Factor Causes Drought and Heat Sensitivity in Rice. Int J Mol Sci 2020; 21:ijms21072288. [PMID: 32225072 PMCID: PMC7177362 DOI: 10.3390/ijms21072288] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/15/2020] [Accepted: 03/23/2020] [Indexed: 12/22/2022] Open
Abstract
Rice (Oryza sativa) responds to various abiotic stresses during growth. Plant-specific NAM, ATAF1/2, and CUC2 (NAC) transcription factors (TFs) play an important role in controlling numerous vital growth and developmental processes. To date, 170 NAC TFs have been reported in rice, but their roles remain largely unknown. Herein, we discovered that the TF OsNAC006 is constitutively expressed in rice, and regulated by H2O2, cold, heat, abscisic acid (ABA), indole-3-acetic acid (IAA), gibberellin (GA), NaCl, and polyethylene glycol (PEG) 6000 treatments. Furthermore, knockout of OsNAC006 using the CRISPR-Cas9 system resulted in drought and heat sensitivity. RNA sequencing (RNA-seq) transcriptome analysis revealed that OsNAC006 regulates the expression of genes mainly involved in response to stimuli, oxidoreductase activity, cofactor binding, and membrane-related pathways. Our findings elucidate the important role of OsNAC006 in drought responses, and provide valuable information for genetic manipulation to enhance stress tolerance in future plant breeding programs.
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Affiliation(s)
- Bo Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China; (B.W.); (X.W.); (X.H.); (D.Y.); (C.W.); (W.S.)
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China; (Z.Z.); (X.Z.)
| | - Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China; (Z.Z.); (X.Z.)
| | - Xia Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China; (B.W.); (X.W.); (X.H.); (D.Y.); (C.W.); (W.S.)
| | - Xiangyan Han
- College of Life Sciences, Nankai University, Tianjin 300071, China; (B.W.); (X.W.); (X.H.); (D.Y.); (C.W.); (W.S.)
| | - Deshui Yu
- College of Life Sciences, Nankai University, Tianjin 300071, China; (B.W.); (X.W.); (X.H.); (D.Y.); (C.W.); (W.S.)
| | - Chunguo Wang
- College of Life Sciences, Nankai University, Tianjin 300071, China; (B.W.); (X.W.); (X.H.); (D.Y.); (C.W.); (W.S.)
| | - Wenqin Song
- College of Life Sciences, Nankai University, Tianjin 300071, China; (B.W.); (X.W.); (X.H.); (D.Y.); (C.W.); (W.S.)
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China; (Z.Z.); (X.Z.)
| | - Chengbin Chen
- College of Life Sciences, Nankai University, Tianjin 300071, China; (B.W.); (X.W.); (X.H.); (D.Y.); (C.W.); (W.S.)
- Correspondence: (C.C.); (Y.Z.)
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu 610054, China; (Z.Z.); (X.Z.)
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College, Yangzhou University, Yangzhou 225009, China
- Correspondence: (C.C.); (Y.Z.)
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