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Cook LSJ, Briscoe AG, Fonseca VG, Boenigk J, Woodward G, Bass D. Microbial, holobiont, and Tree of Life eDNA/eRNA for enhanced ecological assessment. Trends Microbiol 2024:S0966-842X(24)00173-2. [PMID: 39164135 DOI: 10.1016/j.tim.2024.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 08/22/2024]
Abstract
Microbial environmental DNA and RNA (collectively 'eNA') originate from a diverse and abundant array of microbes present in environmental samples. These eNA signals, largely representing whole organisms, serve as a powerful complement to signals derived from fragments or remnants of larger organisms. Integrating microbial data into the toolbox of ecosystem assessments and biotic indices therefore has the potential to transform how we use eNA data to understand biodiversity dynamics and ecosystem functions, and to inform the next generation of environmental monitoring. Incorporating holobiont and Tree of Life approaches into eNA analyses offers further holistic insight into the range of ecological interactions between microbes and other organisms, paving the way for advancing our understanding of, and ultimately manipulating ecosystem properties pertinent to environmental management, conservation, wildlife health, and food production.
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Affiliation(s)
- Lauren S J Cook
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Royal Holloway University of London, Egham, Surrey TW20 0EX, UK
| | - Andrew G Briscoe
- Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; NatureMetrics, Surrey Research Park, Guildford GU2 7HJ, UK
| | - Vera G Fonseca
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, 45141 Essen, Universitätsstraße 5, Germany
| | - Guy Woodward
- Georgina Mace Centre for the Living Planet, Department of Life Sciences, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science, Barrack Road, Weymouth, Dorset DT4 8UB, UK; Science, The Natural History Museum, Cromwell Road, London SW7 5BD, UK; Biosciences, University of Exeter, Stocker Road, Exeter EX4 4QD, UK.
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2
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Geng Y, Zhou P, Wang Z, Peng C, Li G, Li D. The roles of rare and abundant microbial species in the primary succession of biological soil crusts are differentiated in metal tailings ponds with different states. JOURNAL OF HAZARDOUS MATERIALS 2024; 472:134577. [PMID: 38749248 DOI: 10.1016/j.jhazmat.2024.134577] [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: 04/02/2024] [Revised: 04/27/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024]
Abstract
Tailings ponds formed by long-term accumulation of mineral processing waste have become a global environmental problem. Even worse, tailings ponds are often simply abandoned or landfilled after they cease to be used. This allows pollution to persist and continue to spread in the environment. The significance of primary succession mediated by biological soil crusts for tailings pond remediation has been illustrated by previous studies. However, the process of primary succession may not be the same at different stages during the lifetime of tailings ponds. Therefore, we investigated the environmental differences and the successional characteristics of microbial communities in the primary successional stage of tailings ponds at three different states. The results showed that the primary succession process positively changed the environment of tailings ponds in any state of tailings ponds. The primary successional stage determined the environmental quality more than the state of the tailings pond. In the recently abandoned tailings ponds, abundant species were more subjected to heavy metal stress, while rare species were mainly limited by nutrient content. We found that as the succession progressed, rare species gradually acquired their own community space and became more responsive to environmental stresses. Rare species played an important role in microbial keystone species groups.
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Affiliation(s)
- Yuchen Geng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Panpan Zhou
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhicong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Chengrong Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Genbao Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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3
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Brant RA, Edwards CE, Reid JL, Bassüner B, Delfeld B, Dell N, Mangan SA, de la Paz Bernasconi Torres V, Albrecht MA. Restoration age affects microbial-herbaceous plant interactions in an oak woodland. Ecol Evol 2024; 14:e11360. [PMID: 38706936 PMCID: PMC11066493 DOI: 10.1002/ece3.11360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
In degraded ecosystems, soil microbial communities (SMCs) may influence the outcomes of ecological restoration. Restoration practices can affect SMCs, though it is unclear how variation in the onset of restoration activities in woodlands affects SMCs, how those SMCs influence the performance of hard-to-establish woodland forbs, and how different woodland forbs shape SMCs. In this study, we quantified soil properties and species abundances in an oak woodland restoration chronosequence (young, intermediate, and old restorations). We measured the growth of three woodland forb species when inoculated with live whole-soil from young, intermediate, or old restorations. We used DNA metabarcoding to characterize SMCs of each inoculum treatment and the soil after conditioning by each plant species. Our goals were to (1) understand how time since the onset of restoration affected soil abiotic properties, plant communities, and SMCs in a restoration chronosequence, (2) test growth responses of three forb species to whole-soil inoculum from restoration sites, and (3) characterize changes in SMCs before and after conditioning by each forb species. Younger restored woodlands had greater fire-sensitive tree species and lower concentrations of soil phosphorous than intermediate or older restored woodlands. Bacterial and fungal soil communities varied significantly among sites. Forbs exhibited the greatest growth in soil from the young restoration. Each forb species developed a unique soil microbial community. Our results highlight how restoration practices affect SMCs, which can in turn affect the growth of hard-to-establish forb species. Our results also highlight that the choice of forb species can alter SMCs, which could have long-term potential consequences for restoration success.
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Affiliation(s)
| | | | - John Leighton Reid
- Missouri Botanical GardenSt. LouisMissouriUSA
- Present address:
School of Plant and Environmental SciencesVirginia TechBlacksburgVirginiaUSA
| | | | | | - Noah Dell
- Missouri Botanical GardenSt. LouisMissouriUSA
| | - Scott A. Mangan
- Department of Biological SciencesArkansas State UniversityJonesboroArkansasUSA
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Chen Y, Li W, Cai X, Li B, Zhan F, Zu Y, He Y. Organic Materials Promote Rhododendron simsii Growth and Rhizosphere Soil Properties in a Lead-Zinc Mining Wasteland. PLANTS (BASEL, SWITZERLAND) 2024; 13:891. [PMID: 38592957 PMCID: PMC10975995 DOI: 10.3390/plants13060891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 03/17/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The mining of metal minerals generates considerable mining wasteland areas, which are characterized by poor soil properties that hinder plant growth. In this study, a field plot experiment was carried out in the mining wasteland of the Lanping lead-zinc mine in Yunnan Province to study the effects of applying three organic materials-biochar (B), organic fertilizer (OF), and sludge (S)-at concentrations of 1% (mass fraction), on promoting the soil of mining wasteland and the growth of two plant varieties (Huolieniao and Yingshanhong). The results showed that the amount of available nutrients in the surface soil of a mining wasteland could be considerably increased by S and OF compared to the control check (CK). In the rhizosphere soils of two Rhododendron simsii varieties, the application of S increased the available phosphorus (P) content by 66.4% to 108.8% and the alkali-hydrolyzed nitrogen (N) content by 61.7% to 295.5%. However, the contents of available cadmium (Cd) and available lead (Pb) were reduced by 17.1% to 32.0% and 14.8% to 19.0%, respectively. Moreover, three organic materials increased the photosynthetic rate and biomass of two R. simsii varieties. Specifically, OF and S were found to significantly increase the biomass of R. simsii. Organic materials have direct impacts on the increased plant height and biomass of R. simsii. Additionally, organic materials indirectly contribute to the growth of R. simsii by reducing the content of available Cd and available Pb in rhizosphere soil while increasing the content of available nutrients according to the structural equation model (SEM). Overall, S can stabilize Cd and Pb, increase soil nutrient contents, and promote the growth of R. simsii effectively, and has great potential in the vegetation reconstruction of mining wasteland.
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Affiliation(s)
- Yunchun Chen
- College of Water Conservancy, Yunnan Agricultural University, Kunming 650201, China;
| | - Wei Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (X.C.); (B.L.); (F.Z.); (Y.Z.)
| | - Xinchen Cai
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (X.C.); (B.L.); (F.Z.); (Y.Z.)
| | - Bo Li
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (X.C.); (B.L.); (F.Z.); (Y.Z.)
| | - Fangdong Zhan
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (X.C.); (B.L.); (F.Z.); (Y.Z.)
| | - Yanqun Zu
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (X.C.); (B.L.); (F.Z.); (Y.Z.)
| | - Yongmei He
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201, China; (W.L.); (X.C.); (B.L.); (F.Z.); (Y.Z.)
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Lines R, Juggernauth M, Peverley G, Keating J, Simpson T, Mousavi-Derazmahalleh M, Bunce M, Berry TE, Taysom A, Bernardino AF, Whittle P. A large scale temporal and spatial environmental DNA biodiversity survey of marine vertebrates in Brazil following the Fundão tailings dam failure. MARINE ENVIRONMENTAL RESEARCH 2023; 192:106239. [PMID: 37926039 DOI: 10.1016/j.marenvres.2023.106239] [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: 07/01/2023] [Revised: 10/19/2023] [Accepted: 10/22/2023] [Indexed: 11/07/2023]
Abstract
Seawater contains a wealth of genetic information, representing the biodiversity of numerous species residing within a particular marine habitat. Environmental DNA (eDNA) metabarcoding offers a cost effective, non-destructive method for large scale monitoring of environments, as diverse taxonomic groups are detected using metabarcoding assays. A large-scale eDNA monitoring program of marine vertebrates was conducted across three sampling seasons (Spring 2018, Autumn 2019; Spring 2019) in coastal waters of Brazil. The program was designed to investigate eDNA as a testing method for long term monitoring of marine vertebrates following the Fundão tailings dam failure in November 2015. While no baseline samples were available prior to the dam failure there is still value in profiling the taxa that use the impacted area and the trajectory of recovery. A total of 40 sites were sampled around the mouths of eight river systems, covering approximately 500 km of coastline. Metabarcoding assays targeting the mitochondrial genes 16S rRNA and COI were used to detect fish, marine mammals and elasmobranchs. We detected temporal differences between seasons and spatial differences between rivers/estuaries sampled. Overall, the largest eDNA survey in Brazil to date revealed 69 families from Class Actinopterygii (fish), 15 species from Class Chondrichthyes (sharks and rays), 4 species of marine and estuarine mammals and 23 species of conservation significance including 2 species of endangered dolphin. Our large-scale study reinforces the value eDNA metabarcoding can bring when monitoring the biodiversity of coastal environments and demonstrates the importance of collection of time-stamped environmental samples to better understand the impacts of anthropogenic activities.
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Affiliation(s)
- Rose Lines
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia.
| | | | - Georgia Peverley
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia
| | | | - Tiffany Simpson
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Mahsa Mousavi-Derazmahalleh
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia; Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Michael Bunce
- Trace and Environmental DNA laboratory, Curtin University, Perth, Western Australia, Australia
| | - Tina E Berry
- eDNA frontiers, Curtin University, Perth, Western Australia, Australia
| | | | - Angelo F Bernardino
- Grupo de Ecologia Bentônica, Universidade Federal do Espirito Santo, Vitória, ES, Brazil
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Shu X, Liu W, Hu Y, Xia L, Fan K, Zhang Y, Zhang Y, Zhou W. Ecosystem multifunctionality and soil microbial communities in response to ecological restoration in an alpine degraded grassland. FRONTIERS IN PLANT SCIENCE 2023; 14:1173962. [PMID: 37593047 PMCID: PMC10431941 DOI: 10.3389/fpls.2023.1173962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/07/2023] [Indexed: 08/19/2023]
Abstract
Linkages between microbial communities and multiple ecosystem functions are context-dependent. However, the impacts of different restoration measures on microbial communities and ecosystem functioning remain unclear. Here, a 14-year long-term experiment was conducted using three restoration modes: planting mixed grasses (MG), planting shrub with Salix cupularis alone (SA), and planting shrub with Salix cupularis plus planting mixed grasses (SG), with an extremely degraded grassland serving as the control (CK). Our objective was to investigate how ecosystem multifunctionality and microbial communities (diversity, composition, and co-occurrence networks) respond to different restoration modes. Our results indicated that most of individual functions (i.e., soil nutrient contents, enzyme activities, and microbial biomass) in the SG treatment were significantly higher than in the CK treatment, and even higher than MG and SA treatments. Compared with the CK treatment, treatments MG, SA, and SG significantly increased the multifunctionality index on average by 0.57, 0.23 and 0.76, respectively. Random forest modeling showed that the alpha-diversity and composition of bacterial communities, rather than fungal communities, drove the ecosystem multifunctionality. Moreover, we found that both the MG and SG treatments significantly improved bacterial network stability, which exhabited stronger correlations with ecosystem multifunctionality compared to fungal network stability. In summary, this study demonstrates that planting shrub and grasses altogether is a promising restoration mode that can enhance ecosystem multifunctionality and improve microbial diversity and stability in the alpine degraded grassland.
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Affiliation(s)
- Xiangyang Shu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Weijia Liu
- Institute of Agricultural Bioenvironment and Energy, Chengdu Academy of Agriculture and Forestry Sciences, Chengdu, China
| | - Yufu Hu
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Longlong Xia
- Institute for Meteorology and Climate Research (IMK-IFU), Karlsruhe Institute of Technology, Garmisch-Partenkirchen, Germany
| | - Kunkun Fan
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Yanyan Zhang
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Yulin Zhang
- Department of Civil Engineering, The University of Hong Kong, Hong Kong SAR, China
| | - Wei Zhou
- College of Resources, Sichuan Agricultural University, Chengdu, China
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Yan K, Luo YH, Li YJ, Du LP, Gui H, Chen SC. Trajectories of soil microbial recovery in response to restoration strategies in one of the largest and oldest open-pit phosphate mine in Asia. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115215. [PMID: 37421785 DOI: 10.1016/j.ecoenv.2023.115215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/20/2023] [Accepted: 06/29/2023] [Indexed: 07/10/2023]
Abstract
Southwestern China has the largest geological phosphorus-rich mountain in the world, which is seriously degraded by mining activities. Understanding the trajectory of soil microbial recovery and identifying the driving factors behind such restoration, as well as conducting corresponding predictive simulations, can be instrumental in facilitating ecological rehabilitation. Here, high-throughput sequencing and machine learning-based approaches were employed to investigate restoration chronosequences under four restoration strategies (spontaneous re-vegetation with or without topsoil; artificial re-vegetation with or without the addition of topsoil) in one of the largest and oldest open-pit phosphate mines worldwide. Although soil phosphorus (P) is extremely high here (max = 68.3 mg/g), some phosphate solubilizing bacteria and mycorrhiza fungi remain as the predominant functional types. Soil stoichiometry ratios (C:P and N:P) closely relate to the bacterial variation, but soil P content contributes less to microbial dynamics. Meanwhile, as restoration age increases, denitrifying bacteria and mycorrhizal fungi significantly increased. Significantly, based on partial least squares path analysis, it was found that the restoration strategy is the primary factor that drives soil bacterial and fungal composition as well as functional types through both direct and indirect effects. These indirect effects arise from factors such as soil thickness, moisture, nutrient stoichiometry, pH, and plant composition. Moreover, its indirect effects constitute the main driving force towards microbial diversity and functional variation. Using a hierarchical Bayesian model, scenario analysis reveals that the recovery trajectories of soil microbes are contingent upon changes in restoration stage and treatment strategy; inappropriate plant allocation may impede the recovery of the soil microbial community. This study is helpful for understanding the dynamics of the restoration process in degraded phosphorus-rich ecosystems, and subsequently selecting more reasonable recovery strategies.
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Affiliation(s)
- Kai Yan
- College of Resources and Environment, Yunnan Agricultural University, Kunming 650201 Yunnan, China
| | - Ya-Huang Luo
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yun-Ju Li
- The State Phosphorus Resource Development and Utilization Engineering Technology Research Centre, Yunnan Phosphate Chemical Group Co. Ltd, Kunming 650607, China
| | - Ling-Pan Du
- The State Phosphorus Resource Development and Utilization Engineering Technology Research Centre, Yunnan Phosphate Chemical Group Co. Ltd, Kunming 650607, China
| | - Heng Gui
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China; Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China.
| | - Si-Chong Chen
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074 Hubei, China; Millennium Seed Bank, Royal Botanic Gardens Kew, Wakehurst, West Sussex RH17 6TN, UK.
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Tessler M, Cunningham SW, Ingala MR, Warring SD, Brugler MR. An Environmental DNA Primer for Microbial and Restoration Ecology. MICROBIAL ECOLOGY 2023; 85:796-808. [PMID: 36735064 DOI: 10.1007/s00248-022-02168-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 12/28/2022] [Indexed: 05/04/2023]
Abstract
Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.
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Affiliation(s)
- Michael Tessler
- Department of Biology, St. Francis College, Brooklyn, NY, USA.
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA.
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA.
| | - Seth W Cunningham
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, NY, 10024, USA
- Department of Biological Sciences, Fordham University, Bronx, NY, 10458, USA
| | - Melissa R Ingala
- Department of Biological Sciences, Fairleigh Dickinson University, Madison, NJ, 07940, USA
| | | | - Mercer R Brugler
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, 10024, USA
- Department of Natural Sciences, University of South Carolina Beaufort, 801 Carteret Street, Beaufort, SC, 29902, USA
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Su J, Ji W, Sun X, Wang H, Kang Y, Yao B. Effects of different management practices on soil microbial community structure and function in alpine grassland. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 327:116859. [PMID: 36450164 DOI: 10.1016/j.jenvman.2022.116859] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/12/2022] [Accepted: 11/20/2022] [Indexed: 06/17/2023]
Abstract
Management practices, such as grazing exclusion and reseeding, have been implemented to mitigate the degradation of grassland. Low grazing intensities and reseeding increase grass production. Nevertheless, few studies have investigated the effects of these measures on the soil microbial community structure and function in the Qinghai Tibetan Plateau (QTP). To reveal the effects of management practices on soil microbes and give a reference to assess and improve ecosystems functions, we here evaluated the impact of various types of grazing (exclusion, seasonal, and traditional), reseeding (annual oat (Avena fatua) grassland (RO) and perennial artificial grassland cultivated >10 y), and integrated restoration (weed control and no-tillage reseeding) measures on soil microbial community structure and function in the QTP. The Shannon-Wiener diversity indices were highest for prokaryotes under RO and for fungi under integrated grassland restoration. Relative Actinobacteria abundance was higher under seasonal grazing than that under integrated grassland restoration. The latter had relatively higher abundances of Betaproteobacteria, Alphaproteobacteria, and Deltaproteobacteria and comparatively lower abundance of Thermoleophilia. There were significantly higher abundances of plant pathogens under seasonal grazing than those under other managements. There were significantly high proportions of pathotrophs and saprotrophs (10.0%) under seasonal and traditional grazing, respectively. The proportion of pathotrophs under integrated restoration (10.0%) was about seven-fold greater than that under grazing exclusion (1.5%). The relative differences among treatments in terms of soil water content, plant biomass, and soil C:N partially explained the differences in their prokaryotic community compositions. Increases in soil organic carbon and C:N may explain the observed changes in the soil fungal communities. The management practices affected soil microorganisms mainly by altering the soil nutrient profile. Grazing attracted specific pathotrophs and saprotrophs while repelling certain plant pathogens. Hence, modulations in soil microbial community structure and function must be considered in the process of planning for the implementation of grassland degradation management measures.
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Affiliation(s)
- Junhu Su
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China; Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Qilianshan Grassland Ecosystem Observation and Research Station, Wuwei, 733200, China.
| | - Weihong Ji
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China; Institute of Natural and Mathematical Sciences, Massey University, Private Bag, North Shore Mail Centre 0632, Auckland, 102 904rad, New Zealand
| | - Xiaomei Sun
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China; College of Resource and Environmental Science, Gansu Agricultural University, Lanzhou, 730070, China
| | - Haifang Wang
- Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China; College of Life Science and Technology, Gansu Agricultural University, Lanzhou, 730070, China
| | - Yukun Kang
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China; Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Qilianshan Grassland Ecosystem Observation and Research Station, Wuwei, 733200, China
| | - Baohui Yao
- College of Grassland Science, Key Laboratory of Grassland Ecosystem (Ministry of Education), Gansu Agricultural University, Lanzhou, 730070, China; Gansu Agricultural University-Massey University Research Centre for Grassland Biodiversity, Gansu Agricultural University, Lanzhou, 730070, China; Gansu Qilianshan Grassland Ecosystem Observation and Research Station, Wuwei, 733200, China
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Alfonzetti M, Doleac S, Mills CH, Gallagher RV, Tetu S. Characterizing Effects of Microbial Biostimulants and Whole-Soil Inoculums for Native Plant Revegetation. Microorganisms 2022; 11:microorganisms11010055. [PMID: 36677347 PMCID: PMC9867050 DOI: 10.3390/microorganisms11010055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 12/19/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Soil microbes play important roles in plant health and ecosystem functioning, however, they can often be disturbed or depleted in degraded lands. During seed-based revegetation of such sites there is often very low germination and seedling establishment success, with recruitment of beneficial microbes to the rhizosphere one potential contributor to this problem. Here we investigated whether Australian native plant species may benefit from planting seed encapsulated within extruded seed pellets amended with one of two microbe-rich products: a commercial vermicast extract biostimulant or a whole-soil inoculum from a healthy reference site of native vegetation. Two manipulative glasshouse trials assessing the performance of two Australian native plant species (Acacia parramattensis and Indigofera australis) were carried out in both unmodified field-collected soil (trial 1) and in the same soil reduced in nutrients and microbes (trial 2). Seedling emergence and growth were compared between pelleted and bare-seeded controls and analyzed alongside soil nutrient concentrations and culturable microbial community assessments. The addition of microbial amendments maintained, but did not improve upon, high levels of emergence in both plant species relative to unamended pellets. In trial 1, mean time to emergence of Acacia parramattensis seedlings was slightly shorter in both amended pellet types relative to the standard pellets, and in trial 2, whole-soil inoculum pellets showed significantly improved growth metrics. This work shows that there is potential for microbial amendments to positively affect native plant emergence and growth, however exact effects are dependent on the type of amendment, the plant species, and the characteristics of the planting site soil.
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Affiliation(s)
- Matthew Alfonzetti
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Sebastien Doleac
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | | | - Rachael V. Gallagher
- Hawkesbury Institute for the Environment, Western Sydney University, Locked Bag 1797, Penrith, NSW 2751, Australia
- Correspondence: (R.V.G.); (S.T.)
| | - Sasha Tetu
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
- Biomolecular Discovery Research Centre, Macquarie University, Sydney, NSW 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia
- Correspondence: (R.V.G.); (S.T.)
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11
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van der Heyde M, Bunce M, Nevill P. Key factors to consider in the use of environmental DNA metabarcoding to monitor terrestrial ecological restoration. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 848:157617. [PMID: 35901901 DOI: 10.1016/j.scitotenv.2022.157617] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/30/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Ecological restoration of terrestrial environments is a globally important process to combat the loss of biodiversity and ecosystem services. Holistic monitoring of restored biota and active management of restoration is necessary to improve restoration processes and outcomes, and provide evidence to stakeholders that targets are being achieved. Increasingly, environmental DNA (eDNA) metabarcoding is used as a restoration monitoring tool because it is able to generate biodiversity data rapidly, accurately, non-destructively, and reliably, on a wide breadth of organisms from soil microbes to mammals. The overall objective of this review is to discuss the key factors to consider in the use of environmental DNA for monitoring of restored terrestrial ecosystems, hopefully improving monitoring, and ultimately, restoration outcomes. We identified that the majority of eDNA based studies of ecosystem restoration are currently conducted in Europe, North America, and Australia, and that almost half of total studies were published in 2021-22. Soil was the most popular sample substrate, soil microbial communities the most targeted taxa, and forests the most studied ecosystem. We suggest there is no 'one size fits all' approach to restoration monitoring using eDNA, and discuss survey design. Factors to consider include substrate selection, sample collection and storage, assay selection, and data interpretation, all of which require careful planning to obtain reliable, and accurate information that can be used for restoration monitoring and decision making. We explore future directions for research and argue that eDNA metabarcoding can be a useful tool in the restoration monitoring 'toolkit', but requires informed application and greater accessibility to data by a wide spectrum of stakeholders.
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Affiliation(s)
- Mieke van der Heyde
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia.
| | - Michael Bunce
- Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia; Institute of Environmental Science and Research (ESR), Kenepuru, Porirua 5022, New Zealand
| | - Paul Nevill
- ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Bentley, GPP Box U1987, Perth, Western Australia 6102, Australia; Trace and Environmental DNA Laboratory, School of Life and Molecular Sciences, Curtin University, GPO Box U1987, Perth, Western Australia 6102, Australia
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12
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Geng Y, Peng C, Wang Z, Huang S, Zhou P, Li D. Insights into the spatiotemporal differences in tailings seepage pollution by assessing the diversity and metabolic functions of the soil microbial community. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 306:119408. [PMID: 35523382 DOI: 10.1016/j.envpol.2022.119408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/29/2022] [Accepted: 04/30/2022] [Indexed: 06/14/2023]
Abstract
The formation of tailings ponds depends on the long-term accumulation of tailing and high terrain. Its seepage pollution characteristics may have gradient variations on spatiotemporal scales. Used three nearby metal tailings ponds with different service times, we aimed to reveal seepage pollution trends on spatiotemporal scales and the response of soil microbial community. The results showed that the degree of seepage pollution was negatively correlated with the distance from the tailings pond on the spatial scale, while the seepage pollution showed higher levels in tailings ponds with longer service times on the temporal scale (RI = 248.04-2109.85). The pollution effect of seepage persisted after the tailings pond was discontinued (RI = 226.72). Soil microbial diversity increased with spatial scale expansion. The proportion of Actinomyces gradually increased and Proteobacteria decreased. Cr (r = 0.21) and Fe (r = 0.22) contributed more to the microbial community changes. Functional predictions showed that pathways related to signal transduction and energy metabolism were more abundant in the tailings pond. In contaminated areas, the proportion of nitrate respiration and cellulolysis functional communities had decreased, and some potentially pathogenic human taxa had accumulated. These results emphasized that there was pollution accumulation on temporal scale and pollution dispersion on spatial scale around tailings ponds, and the response of the microbial community further illustrated these trends.
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Affiliation(s)
- Yuchen Geng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengrong Peng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Zhicong Wang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Shun Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Panpan Zhou
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dunhai Li
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.
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13
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Spatiotemporal Variability of Human Disturbance Impacts on Ecosystem Services in Mining Areas. SUSTAINABILITY 2022. [DOI: 10.3390/su14137547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Human activities pose significant impacts on ecosystem services (ESs) in mining areas, which will continually increase over time and space. However, the mechanism of ES change on spatiotemporal scales post-disturbance remains unclear, especially in the context of global climate change. Here, we conducted a global literature review on the impact of two of the most frequent disturbance factors (mining and restoration) on 27 different ESs, intending to synthesize the impacts of human disturbance on ESs in mining areas via a meta-analysis, and analyze the spatiotemporal variability of ESs after disturbance. We screened 3204 disturbance studies published on the Web of Science between 1950 and 2020 and reviewed 340 in detail. The results of independence test showed that human disturbance had a significant impact on ESs in the mining areas (p < 0.001). The impacts (positive and/or negative) caused by mining and restoration differed considerably among ESs (even on the same ESs). Additionally, spatiotemporal scales of human disturbance were significantly related to spatiotemporal scales of ES change (p < 0.001). We found that the positive and negative impacts of disturbances on ESs may be interconversion under specific spatiotemporal conditions. This seems to be associated with spatiotemporal variability, such as the temporal lag, spatial spillover, and cumulative spatiotemporal effects. Climate changes can lead to further spatiotemporal variability, which highlights the importance of understanding the changes in ESs post-disturbance on spatiotemporal scales. Our research presents recommendations for coping with the twofold pressure of climate change and spatiotemporal variability, to understand how ESs respond to human disturbance at spatiotemporal scales in the future, and manage disturbances to promote sustainable development in mining areas.
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14
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D'Agui HM, van der Heyde ME, Nevill PG, Mousavi‐Derazmahalleh M, Dixon KW, Moreira‐Grez B, Valliere JM. Evaluating biological properties of topsoil for post‐mining ecological restoration: different assessment methods give different results. Restor Ecol 2022. [DOI: 10.1111/rec.13738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Haylee M. D'Agui
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
| | - Mieke E. van der Heyde
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences, Curtin University, Kent Street Bentley Western Australia 6102
| | - Paul G. Nevill
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences, Curtin University, Kent Street Bentley Western Australia 6102
| | - Mahsa Mousavi‐Derazmahalleh
- Trace and Environmental DNA Laboratory School of Molecular and Life Sciences, Curtin University, Kent Street Bentley Western Australia 6102
| | - Kingsley W. Dixon
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
| | - Benjamin Moreira‐Grez
- UWA School of Agriculture and Environment, University of Western Australia, 35 Stirling Highway Crawley Western Australia Australia 6009
| | - Justin M. Valliere
- ARC Centre for Mine Site Restoration School of Molecular and life Sciences, Curtin University, Kent Street Bentley Western Australia Australia 6102
- UWA School of Biological Sciences, University of Western Australia, 35 Stirling Highway Crawley Western Australia Australia 6009
- California State University, Dominguez Hills, 1000 E Victoria Street Carson California USA 90747
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15
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Liddicoat C, Krauss SL, Bissett A, Borrett RJ, Ducki LC, Peddle SD, Bullock P, Dobrowolski MP, Grigg A, Tibbett M, Breed MF. Next generation restoration metrics: Using soil eDNA bacterial community data to measure trajectories towards rehabilitation targets. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 310:114748. [PMID: 35192978 DOI: 10.1016/j.jenvman.2022.114748] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/28/2022] [Accepted: 02/15/2022] [Indexed: 06/14/2023]
Abstract
In post-mining rehabilitation, successful mine closure planning requires specific, measurable, achievable, relevant and time-bound (SMART) completion criteria, such as returning ecological communities to match a target level of similarity to reference sites. Soil microbiota are fundamentally linked to the restoration of degraded ecosystems, helping to underpin ecological functions and plant communities. High-throughput sequencing of soil eDNA to characterise these communities offers promise to help monitor and predict ecological progress towards reference states. Here we demonstrate a novel methodology for monitoring and evaluating ecological restoration using three long-term (>25 year) case study post-mining rehabilitation soil eDNA-based bacterial community datasets. Specifically, we developed rehabilitation trajectory assessments based on similarity to reference data from restoration chronosequence datasets. Recognising that numerous alternative options for microbiota data processing have potential to influence these assessments, we comprehensively examined the influence of standard versus compositional data analyses, different ecological distance measures, sequence grouping approaches, eliminating rare taxa, and the potential for excessive spatial autocorrelation to impact on results. Our approach reduces the complexity of information that often overwhelms ecologically-relevant patterns in microbiota studies, and enables prediction of recovery time, with explicit inclusion of uncertainty in assessments. We offer a step change in the development of quantitative microbiota-based SMART metrics for measuring rehabilitation success. Our approach may also have wider applications where restorative processes facilitate the shift of microbiota towards reference states.
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Affiliation(s)
- Craig Liddicoat
- College of Science and Engineering, Flinders University, Adelaide, Australia; School of Public Health, The University of Adelaide, Adelaide, Australia.
| | - Siegfried L Krauss
- Kings Park Science, Western Australia Department of Biodiversity Conservation and Attractions, Perth, Australia; School of Biological Sciences, University of Western Australia, Perth, Australia
| | | | - Ryan J Borrett
- College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Luisa C Ducki
- College of Science and Engineering, Flinders University, Adelaide, Australia; College of Science, Health, Engineering and Education, Murdoch University, Perth, Australia
| | - Shawn D Peddle
- College of Science and Engineering, Flinders University, Adelaide, Australia
| | | | - Mark P Dobrowolski
- School of Biological Sciences, University of Western Australia, Perth, Australia; Iluka Resources Limited, Perth, Australia; Harry Butler Institute, Murdoch University, Perth, Australia
| | | | - Mark Tibbett
- School of Biological Sciences, University of Western Australia, Perth, Australia; Department of Sustainable Land Management & Soil Research Centre, School of Agriculture, Policy and Development, University of Reading, Berkshire, United Kingdom
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Adelaide, Australia
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16
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Saccò M, Guzik MT, van der Heyde M, Nevill P, Cooper SJB, Austin AD, Coates PJ, Allentoft ME, White NE. eDNA in subterranean ecosystems: Applications, technical aspects, and future prospects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153223. [PMID: 35063529 DOI: 10.1016/j.scitotenv.2022.153223] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/09/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Monitoring of biota is pivotal for the assessment and conservation of ecosystems. Environments worldwide are being continuously and increasingly exposed to multiple adverse impacts, and the accuracy and reliability of the biomonitoring tools that can be employed shape not only the present, but more importantly, the future of entire habitats. The analysis of environmental DNA (eDNA) metabarcoding data provides a quick, affordable, and reliable molecular approach for biodiversity assessments. However, while extensively employed in aquatic and terrestrial surface environments, eDNA-based studies targeting subterranean ecosystems are still uncommon due to the lack of accessibility and the cryptic nature of these environments and their species. Recent advances in genetic and genomic analyses have established a promising framework for shedding new light on subterranean biodiversity and ecology. To address current knowledge and the future use of eDNA methods in groundwaters and caves, this review explores conceptual and technical aspects of the application and its potential in subterranean systems. We briefly introduce subterranean biota and describe the most used traditional sampling techniques. Next, eDNA characteristics, application, and limitations in the subsurface environment are outlined. Last, we provide suggestions on how to overcome caveats and delineate some of the research avenues that will likely shape this field in the near future. We advocate that eDNA analyses, when carefully conducted and ideally combined with conventional sampling techniques, will substantially increase understanding and enable crucial expansion of subterranean community characterisation. Given the importance of groundwater and cave ecosystems for nature and humans, eDNA can bring to the surface essential insights, such as study of ecosystem assemblages and rare species detection, which are critical for the preservation of life below, as well as above, the ground.
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Affiliation(s)
- Mattia Saccò
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia.
| | - Michelle T Guzik
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Mieke van der Heyde
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Paul Nevill
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; ARC Centre for Mine Site Restoration, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
| | - Steven J B Cooper
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia; Evolutionary Biology Unit, South Australian Museum, North Terrace, Adelaide 5000, SA, Australia
| | - Andrew D Austin
- Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, The University of Adelaide, Adelaide 5005, SA, Australia
| | - Peterson J Coates
- Bedford Institute of Oceanography, Fisheries and Oceans Canada, 1 Challenger Drive, 1006, Dartmouth, Nova Scotia B2Y 4A2, Canada
| | - Morten E Allentoft
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia; Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Øster Voldgade 5-7, Copenhagen, Denmark
| | - Nicole E White
- Subterranean Research and Groundwater Ecology (SuRGE) Group, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth 6102, WA, Australia
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17
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Peddle SD, Bissett A, Borrett RJ, Bullock P, Gardner MG, Liddicoat C, Tibbett M, Breed MF, Krauss SL. Soil
DNA
chronosequence analysis shows bacterial community re‐assembly following post‐mining forest rehabilitation. Restor Ecol 2022. [DOI: 10.1111/rec.13706] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shawn D. Peddle
- College of Science and Engineering Flinders University Bedford Park SA Australia
| | | | - Ryan J. Borrett
- Environmental and Conservation Sciences Murdoch University Murdoch WA Australia
| | | | - Michael G. Gardner
- College of Science and Engineering Flinders University Bedford Park SA Australia
- Evolutionary Biology Unit, South Australian Museum Adelaide SA Australia
| | - Craig Liddicoat
- College of Science and Engineering Flinders University Bedford Park SA Australia
- School of Public Health The University of Adelaide Adelaide Australia
| | - Mark Tibbett
- Department of Sustainable Land Management & Soil Research Centre, School of Agriculture, Policy and Development University of Reading Berkshire United Kingdom
- School of Biological Sciences The University of Western Australia Crawley WA Australia
| | - Martin F. Breed
- College of Science and Engineering Flinders University Bedford Park SA Australia
| | - Siegfried L. Krauss
- Kings Park Science, Department of Biodiversity Conservation and Attractions Perth WA Australia
- School of Biological Sciences The University of Western Australia Crawley WA Australia
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18
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Metabarcoding under Brine: Microbial Ecology of Five Hypersaline Lakes at Rottnest Island (WA, Australia). WATER 2021. [DOI: 10.3390/w13141899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hypersaline ecosystems—aquatic environments where concentration of salt exceeds 35 g L−1—host microbial communities that are highly specialised to cope with these extreme conditions. However, our knowledge on the taxonomic diversity and functional metabolisms characterising microbial communities in the water columns of hypersaline ecosystems is still limited, and this may compromise the future preservation of these unique environments. DNA metabarcoding provides a reliable and affordable tool to investigate environmental dynamics of aquatic ecosystems, and its use in brine can be highly informative. Here, we make use of bacterial 16S metabarcoding techniques combined with hydrochemical analyses to investigate the microbial patterns (diversity and functions) from five hypersaline lakes located at Rottnest Island (WA). Our results indicate lake-driven microbial aquatic assemblages that are characterised by taxonomically and functionally moderately to extremely halophilic groups, with TDS (total dissolved solids) and alkalinity amongst the most influential parameters driving the community patterns. Overall, our findings suggest that DNA metabarcoding allows rapid but reliable ecological assessment of the hypersaline aquatic microbial communities at Rottnest Island. Further studies involving different hypersaline lakes across multiple seasons will help elucidate the full extent of the potential of this tool in brine.
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Abstract
Land degradation has become one of the major global environmental problems threatening human well-being. Whether degraded land can be restored has a profound effect on the achievement of the 2030 UN Sustainable Development Goals. Therefore, the ways by which to identify the current research status and potential research topics in the massive scientific literature data in the field of land degradation is a crucial issue for scientific research institutions in various countries. In view of the shortcomings in the current research on the thematic evolution and thematic and thematic prediction, such as the ignorance of random features during scientific innovation, the defects of manual classification, and the difficulty of identifying technical terms, this research proposes a new combined method. First, the Latent Dirichlet Allocation (LDA) algorithm in machine learning is used to capture the potential clustering of themes in the literature sample set of land degradation research. The distribution characteristics and evolution of themes in each period are then analyzed. The method is combined with the Hidden Markov Model (HMM), which contains double stochastic process to quantitatively predict the trend of future thematic evolution. Finally, the above-mentioned combined method is used to analyze the evolution characteristics and future development trends of the themes in the field of land degradation. Comparative experiments show that the method in this study is effective and practical. The research results show that rangeland degradation, surface temperature, island, soil degradation, water quality, crop productivity and restoration are important research topics in the field of land degradation in the future. In addition, based on the advantages of this model, this model can be widely used in the thematic evolution and prediction analysis of different research fields in land use science.
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Francioli D, Lentendu G, Lewin S, Kolb S. DNA Metabarcoding for the Characterization of Terrestrial Microbiota-Pitfalls and Solutions. Microorganisms 2021; 9:361. [PMID: 33673098 PMCID: PMC7918050 DOI: 10.3390/microorganisms9020361] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Soil-borne microbes are major ecological players in terrestrial environments since they cycle organic matter, channel nutrients across trophic levels and influence plant growth and health. Therefore, the identification, taxonomic characterization and determination of the ecological role of members of soil microbial communities have become major topics of interest. The development and continuous improvement of high-throughput sequencing platforms have further stimulated the study of complex microbiota in soils and plants. The most frequently used approach to study microbiota composition, diversity and dynamics is polymerase chain reaction (PCR), amplifying specific taxonomically informative gene markers with the subsequent sequencing of the amplicons. This methodological approach is called DNA metabarcoding. Over the last decade, DNA metabarcoding has rapidly emerged as a powerful and cost-effective method for the description of microbiota in environmental samples. However, this approach involves several processing steps, each of which might introduce significant biases that can considerably compromise the reliability of the metabarcoding output. The aim of this review is to provide state-of-the-art background knowledge needed to make appropriate decisions at each step of a DNA metabarcoding workflow, highlighting crucial steps that, if considered, ensures an accurate and standardized characterization of microbiota in environmental studies.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
| | - Guillaume Lentendu
- Laboratory of Soil Biodiversity, University of Neuchâtel, Rue Emile-Argand 11, 2000 Neuchâtel, Switzerland;
| | - Simon Lewin
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Eberswalder Str. 84, 15374 Müncheberg, Germany; (S.L.); (S.K.)
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