1
|
Gruppuso L, Receveur JP, Fenoglio S, Bona F, Benbow ME. Hidden Decomposers: the Role of Bacteria and Fungi in Recently Intermittent Alpine Streams Heterotrophic Pathways. MICROBIAL ECOLOGY 2023; 86:1499-1512. [PMID: 36646914 PMCID: PMC10497695 DOI: 10.1007/s00248-023-02169-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
Abstract
The frequency of flow intermittency and drying events in Alpine rivers is expected to increase due to climate change. These events can have significant consequences for stream ecological communities, though the effects of reduced flow conditions on microbial communities of decomposing allochthonous leaf material require additional research. In this study, we investigated the bacterial and fungal communities associated with the decomposition of two common species of leaf litter, chestnut (Castanea sativa), and oak (Quercus robur). A sampling of experimentally placed leaf bags occurred over six collection dates (up to 126 days after placement) at seven stream sites in the Western Italian Alps with historically different flow conditions. Leaf-associated bacterial and fungal communities were identified using amplicon-based, high-throughput sequencing. Chestnut and oak leaf material harbored distinct bacterial and fungal communities, with a number of taxonomic groups differing in abundance, though bacterial community structure converged later in decomposition. Historical flow conditions (intermittent vs perennial rivers) and observed conditions (normal flow, low flow, ongoing drying event) had weaker effects on bacterial and fungal communities compared to leaf type and collection date (i.e., length of decomposition). Our findings highlight the importance of leaf characteristics (e.g., C:N ratios, recalcitrance) to the in-stream conditioning of leaf litter and a need for additional investigations of drying events in Alpine streams. This study provides new information on the microbial role in leaf litter decomposition with expected flow changes associated with a global change scenario.
Collapse
Affiliation(s)
- L Gruppuso
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy.
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy.
| | - J P Receveur
- Institute for Genome Sciences, University of Maryland, Baltimore, MD, USA
| | - S Fenoglio
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy
| | - F Bona
- Department of Life Sciences and Systems Biology, University of Turin, Via Accademia Albertina 13, 10123, Turin, Italy
- Centro per lo Studio dei Fiumi Alpini (ALPSTREAM - Alpine Stream Research Center), Ostana, (CN), Italy
| | - M E Benbow
- Department of Entomology, Michigan State University, East Lansing, MI, USA
- Department of Osteopathic Medical Specialties, Michigan State University, East Lansing, MI, USA
- Ecology, Evolution and Behavior Program, Michigan State University, East Lansing, MI, USA
| |
Collapse
|
2
|
Targueta CP, Antunes AM, Machado KB, Fernandes JG, Telles MPDEC, Vieira LCG, Logares R, Nabout JC, Soares TN. Diversity of eukaryotic and prokaryotic microbiota revealed by metabarcoding in Neotropical floodplain lakes. AN ACAD BRAS CIENC 2023; 95:e20201578. [PMID: 37585965 DOI: 10.1590/0001-3765202320201578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/27/2023] [Indexed: 08/18/2023] Open
Abstract
The diversity of eukaryotic and prokaryotic communities has been assessed by morphological and genetic approaches, which are used to characterize the microbiota in different environments. Here, planktonic prokaryotic and eukaryotic communities of the Araguaia River, located in the Central region of Brazil, were analyzed based on metabarcoding analysis of rRNA genes to evaluate the diversity of these groups in tropical floodplain lakes. Also, we tested their spatial concordance throughout the Araguaia river. Water samples were collected from 8 floodplain lakes in Araguaia River. The 16S and 18S rRNA genes were amplified and sequenced using Illumina MiSeq. For eukaryotes, 34,242 merged reads were obtained and 225 distinct OTUs were delineated, of which 106 OTUs were taxonomically classified. For prokaryotes, 26,426 sequences were obtained and 351 OTUs were detected. Of them, 231 were classified in at least one taxonomic category. The most representative eukaryotes belonged to Ciliophora, Chlorophyta and Charophyta. The prokaryotic phylum with the most OTUs classified were Proteobacteria, Actinobacteria and Bacteroidetes. The lakes did not show spatial concordance when comparing the similarity between their microbiota. The knowledge of freshwater biodiversity using DNA sequencing for important rivers, such as Araguaia River, can improve microbiota inventories of tropical biodiversity hotspots.
Collapse
Affiliation(s)
- Cíntia P Targueta
- Programa de Pós-Graduação em Biotecnologia e Biodiversidade, Universidade Federal de Goiás, Instituto de Ciências Biológicas, Avenida Esperança, s/n, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Adriana M Antunes
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Avenida Esperança, s/n, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| | - Karine B Machado
- Universidade Estadual de Goiás (UEG), Campus Central, BR 153, Fazenda Barreiro do Meio, N° 3105, 75132-903 Anápolis, GO, Brazil
| | - Jordana G Fernandes
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Rua 235, 722, Setor Leste Universitário, 74605-050 Goiânia, GO, Brazil
| | - Mariana P DE C Telles
- Escola de Ciências Médicas e da Vida, Pontifícia Universidade Católica de Goiás, Rua 235, 722, Setor Leste Universitário, 74605-050 Goiânia, GO, Brazil
| | - Ludgero C Galli Vieira
- Universidade de Brasília (UnB), Campus Planaltina, Área Universitária 1, Vila Nossa Senhora de Fátima, 73345-010 Planaltina, DF, Brazil
| | - Ramiro Logares
- Instituto de Ciências del Mar, Departamento de Biologia Marinha e Oceanografia CSIC, 08003, Barcelona, Spain
| | - João C Nabout
- Universidade Estadual de Goiás (UEG), Campus Central, BR 153, Fazenda Barreiro do Meio, N° 3105, 75132-903 Anápolis, GO, Brazil
| | - Thannya N Soares
- Universidade Federal de Goiás, Instituto de Ciências Biológicas, Avenida Esperança, s/n, Campus Samambaia, 74690-900 Goiânia, GO, Brazil
| |
Collapse
|
3
|
Ortmeyer F, Guerreiro MA, Begerow D, Banning A. Modified microbiology through enhanced denitrification by addition of various organic substances-temperature effect. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:60282-60293. [PMID: 37022539 PMCID: PMC10163118 DOI: 10.1007/s11356-023-26784-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 03/29/2023] [Indexed: 05/08/2023]
Abstract
Worldwide, the environmental nitrate (NO3-) problem is increasingly coming into focus. These increases in NO3- concentration result mainly from agricultural inputs and are further exacerbated by decreasing and finite geogenic NO3- degradation capacity in aquifers. Thus, treatment methods are becoming more and more important. In this study, the effects of enhanced denitrification with addition of organic carbon (C) on thereby autochthonous occurring microbiology and compared at room temperature as well as 10 °C were investigated. Incubation of bacteria and fungi was carried out using natural sediments without degradation capacity and groundwater with high NO3- concentrations. Addition of the four applied substrates (acetate, glucose, ascorbic acid, and ethanol) results in major differences in microbial community. Cooling to 10 °C changes the microbiology again. Relative abundances of bacteria are strongly influenced by temperature, which is probably the explanation for different denitrification rates. Fungi are much more sensitive to the milieu change with organic C. Different fungi taxa preferentially occur at one of the two temperature approaches. Major modifications of the microbial community are mainly observed whose denitrification rates strongly depend on the temperature effect. Therefore, we assume a temperature optimum of enhanced denitrification specific to each substrate, which is influenced by the microbiology.
Collapse
Affiliation(s)
- Felix Ortmeyer
- Hydrogeology Department, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany.
- Geological Survey of Denmark and Greenland, Øster Voldgade 10, 1350 Copenhagen and Universitetsbyen 81, 8000, Aarhus, Denmark.
| | - Marco Alexandre Guerreiro
- Department of Evolution of Plants and Fungi, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
- Environmental Genomics, Christian-Albrechts University of Kiel, Am Botanischen Garten 1-9, 24118, Kiel, Germany
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Str. 2, 24306, Plön, Germany
| | - Dominik Begerow
- Department of Evolution of Plants and Fungi, Ruhr-Universität Bochum, Universitätsstraße 150, 44801, Bochum, Germany
- University of Hamburg, Institute of Plant Sciences and Microbiology, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Andre Banning
- School of Biological, Earth and Environmental Sciences, University College Cork, Distillery Fields, North Mall, Cork, T23 N73K, Ireland
- University College Cork, Environmental Research Institute, Lee Road, Cork, T23 XE10, Ireland
| |
Collapse
|
4
|
Linking processes to community functions—insights into litter decomposition combining fungal metatranscriptomics and environmental NMR profiling. Mycol Prog 2023. [DOI: 10.1007/s11557-022-01859-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
AbstractIn forest ecosystems, decomposition is essential for carbon and nutrient cycling and therefore a key process for ecosystem functioning. During the decomposition process, litter chemistry, involved decomposer organisms, and enzymatic activity change interdependently. Chemical composition of the litter is the most complex and dynamic component in the decomposition process and therefore challenging to assess holistically. In this study, we aimed to characterize chemical shifts during decomposition and link them to changes in decomposer fungal activity. We characterized the chemical composition of freshly fallen autumn leaves of European beech (Fagus sylvatica) and the corresponding leaf litter after 1 year of decomposition by proton nuclear magnetic resonance spectroscopy. We further tested the applicability of spiking experiments for qualitative and quantitative characterization of leaves and litter chemistry. The composition and transcriptional activity of fungal communities was assessed by high-throughput Illumina sequencing in the same litter samples. We were able to distinguish freshly fallen leaves from 1-year-old litter based on their chemical composition. Chemical composition of leaves converged among regions with progressing decomposition. Fungal litter communities differed in composition among regions, but they were functionally redundant according to the expression of genes encoding litter degrading enzymes (CAZymes). Fungi of the saprotrophic genera Mycena and Chalara correlated with transcription of litter-degrading CAZymes in 1-year-old litter. Forestry measures influenced the diversity and transcription rate of the detected CAZymes transcripts in litter. Their expression was primarily predicted by composition of the soluble chemical fraction of the litter. Environmental NMR fingerprints thus proved valuable for inferring ecological contexts. We propose and discuss a holistic framework to link fungal activity, enzyme expression, and chemical composition.
Collapse
|
5
|
Interaction between growth environment and host progeny shape fungal endophytic assemblages in transplanted Fagus sylvatica. FUNGAL ECOL 2022. [DOI: 10.1016/j.funeco.2022.101175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
6
|
Kambach S, Sadlowski C, Peršoh D, Guerreiro MA, Auge H, Röhl O, Bruelheide H. Foliar Fungal Endophytes in a Tree Diversity Experiment Are Driven by the Identity but Not the Diversity of Tree Species. Life (Basel) 2021; 11:1081. [PMID: 34685452 PMCID: PMC8539603 DOI: 10.3390/life11101081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 10/07/2021] [Accepted: 10/08/2021] [Indexed: 01/05/2023] Open
Abstract
Symbiotic foliar fungal endophytes can have beneficial effects on host trees and might alleviate climate-induced stressors. Whether and how the community of foliar endophytes is dependent on the tree neighborhood is still under debate with contradicting results from different tree diversity experiments. Here, we present our finding regarding the effect of the tree neighborhood from the temperate, densely planted and 12-years-old Kreinitz tree diversity experiment. We used linear models, redundancy analysis, Procrustes analysis and Holm-corrected multiple t-tests to quantify the effects of the plot-level tree neighborhood on the diversity and composition of foliar fungal endophytes in Fagus sylvatica, Quercus petraea and Picea abies. Against our expectations, we did not find an effect of tree diversity on endophyte diversity. Endophyte composition, however, was driven by the identity of the host species. Thirteen endophytes where overabundant in tree species mixtures, which might indicate frequent spillover or positive interactions between foliar endophytes. The independence of the diversity of endophytes from the diversity of tree species might be attributed to the small plot size and the high density of tree individuals. However, the mechanistic causes for these cryptic relationships still remain to be uncovered.
Collapse
Affiliation(s)
- Stephan Kambach
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany;
| | - Christopher Sadlowski
- Faculty of Biology and Biotechnology, Ruhr University of Bochum, Universitätsstraße 150, 44801 Bochum, Germany; (C.S.); (D.P.); (M.A.G.); (O.R.)
| | - Derek Peršoh
- Faculty of Biology and Biotechnology, Ruhr University of Bochum, Universitätsstraße 150, 44801 Bochum, Germany; (C.S.); (D.P.); (M.A.G.); (O.R.)
| | - Marco Alexandre Guerreiro
- Faculty of Biology and Biotechnology, Ruhr University of Bochum, Universitätsstraße 150, 44801 Bochum, Germany; (C.S.); (D.P.); (M.A.G.); (O.R.)
| | - Harald Auge
- Department of Community Ecology, Helmholtz Centre for Environmental Research—UFZ, Theodor-Lieser-Str. 4, 06120 Halle, Germany;
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Oliver Röhl
- Faculty of Biology and Biotechnology, Ruhr University of Bochum, Universitätsstraße 150, 44801 Bochum, Germany; (C.S.); (D.P.); (M.A.G.); (O.R.)
| | - Helge Bruelheide
- Institute of Biology/Geobotany and Botanical Garden, Martin Luther University Halle-Wittenberg, Am Kirchtor 1, 06108 Halle, Germany;
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| |
Collapse
|
7
|
Dahl MB, Peršoh D, Jentsch A, Kreyling J. Root-Associated Mycobiomes of Common Temperate Plants (Calluna vulgaris and Holcus lanatus) Are Strongly Affected by Winter Climate Conditions. MICROBIAL ECOLOGY 2021; 82:403-415. [PMID: 33452897 PMCID: PMC8384817 DOI: 10.1007/s00248-020-01667-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 12/16/2020] [Indexed: 05/06/2023]
Abstract
Winter temperatures are projected to increase in Central Europe. Subsequently, snow cover will decrease, leading to increased soil temperature variability, with potentially different consequences for soil frost depending on e.g. altitude. Here, we experimentally evaluated the effects of increased winter soil temperature variability on the root associated mycobiome of two plant species (Calluna vulgaris and Holcus lanatus) at two sites in Germany; a colder and wetter upland site with high snow accumulation and a warmer and drier lowland site, with low snow accumulation. Mesocosm monocultures were set-up in spring 2010 at both sites (with soil and plants originating from the lowland site). In the following winter, an experimental warming pulse treatment was initiated by overhead infrared heaters and warming wires at the soil surface for half of the mesocosms at both sites. At the lowland site, the warming treatment resulted in a reduced number of days with soil frost as well as increased the average daily temperature amplitude. Contrary, the treatment caused no changes in these parameters at the upland site, which was in general a much more frost affected site. Soil and plant roots were sampled before and after the following growing season (spring and autumn 2011). High-throughput sequencing was used for profiling of the root-associated fungal (ITS marker) community (mycobiome). Site was found to have a profound effect on the composition of the mycobiome, which at the upland site was dominated by fast growing saprotrophs (Mortierellomycota), and at the lowland site by plant species-specific symbionts (e.g. Rhizoscyphus ericae and Microdochium bolleyi for C. vulgaris and H. lanatus respectively). The transplantation to the colder upland site and the temperature treatment at the warmer lowland site had comparable consequences for the mycobiome, implying that winter climate change resulting in higher temperature variability has large consequences for mycobiome structures regardless of absolute temperature of a given site.
Collapse
Affiliation(s)
- Mathilde Borg Dahl
- Institute of Microbiology, Center for Functional Genomics of Microbes, University of Greifswald, Felix-Hausdorff-Str. 8, 17487, Greifswald, Mecklenburg-Vorpommern, Germany.
| | - Derek Peršoh
- Geobotanik, Ruhr-Universität Bochum, Bochum, Germany
| | - Anke Jentsch
- Disturbance Ecology, Bayreuth Center of Ecology and Environmental Research BayCEER, University of Bayreuth, Bayreuth, Germany
| | - Jürgen Kreyling
- Institute of Botany and Landscape ecology, University of Greifswald, Greifswald, Germany
| |
Collapse
|
8
|
Sedimentary Ancient DNA (sedaDNA) Reveals Fungal Diversity and Environmental Drivers of Community Changes throughout the Holocene in the Present Boreal Lake Lielais Svētiņu (Eastern Latvia). Microorganisms 2021; 9:microorganisms9040719. [PMID: 33807307 PMCID: PMC8066534 DOI: 10.3390/microorganisms9040719] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/27/2021] [Accepted: 03/27/2021] [Indexed: 01/16/2023] Open
Abstract
Fungi are ecologically important in several ecosystem processes, yet their community composition, ecophysiological roles, and responses to changing environmental factors in historical sediments are rarely studied. Here we explored ancient fungal DNA from lake Lielais Svētiņu sediment throughout the Holocene (10.5 kyr) using the ITS metabarcoding approach. Our data revealed diverse fungal taxa and smooth community changes during most of the Holocene with rapid changes occurring in the last few millennia. More precisely, plankton parasitic fungi became more diverse from the Late Holocene (2–4 kyr) which could be related to a shift towards a cooler climate. The Latest Holocene (~2 kyr) showed a distinct increase in the richness of plankton parasites, mycorrhizal, and plant pathogenic fungi which can be associated with an increased transfer rate of plant material into the lake and blooms of planktonic organisms influenced by increased, yet moderate, human impact. Thus, major community shifts in plankton parasites and mycorrhizal fungi could be utilized as potential paleo-variables that accompany host-substrate dynamics. Our work demonstrates that fungal aDNA with predicted ecophysiology and host specificity can be employed to reconstruct both aquatic and surrounding terrestrial ecosystems and to estimate the influence of environmental change.
Collapse
|
9
|
Gossner MM, Beenken L, Arend K, Begerow D, Peršoh D. Insect herbivory facilitates the establishment of an invasive plant pathogen. ISME COMMUNICATIONS 2021; 1:6. [PMID: 37938649 PMCID: PMC9723786 DOI: 10.1038/s43705-021-00004-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 01/29/2021] [Accepted: 02/05/2021] [Indexed: 05/17/2023]
Abstract
Plants can be severely affected by insect herbivores and phytopathogenic fungi, but interactions between these plant antagonists are poorly understood. We analysed the impact of feeding damage by the abundant herbivore Orchestes fagi on infection rates of beech (Fagus sylvatica) leaves with Petrakia liobae, an invasive plant pathogenic fungus. The fungus was not detected in hibernating beetles, indicating that O. fagi does not serve as vector for P. liobae, at least not between growing seasons. Abundance of the fungus in beech leaves increased with feeding damage of the beetle and this relationship was stronger for sun-exposed than for shaded leaves. A laboratory experiment revealed sun-exposed leaves to have thicker cell walls and to be more resistant to pathogen infection than shaded leaves. Mechanical damage significantly increased frequency and size of necroses in the sun, but not in shade leaves. Our findings indicate that feeding damage of adult beetles provides entry ports for fungal colonization by removal of physical barriers and thus promotes infection success by pathogenic fungi. Feeding activity by larvae probably provides additional nutrient sources or eases access to substrates for the necrotrophic fungus. Our study exemplifies that invasive pathogens may benefit from herbivore activity, which may challenge forest health in light of climate change.
Collapse
Affiliation(s)
- Martin M Gossner
- Forest Entomology, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland.
- Terrestrial Ecology Research Group, Department of Ecology and Ecosystem Management, Center for Food and Life Sciences Weihenstephan, Technische Universität München, Freising-Weihenstephan, Germany.
- ETH Zurich, Department of Environmental Systems Science, Institute of Terrestrial Ecosystems, Zurich, Switzerland.
| | - Ludwig Beenken
- Forest Protection, Swiss Federal Research Institute WSL, Birmensdorf, Switzerland
| | - Kirstin Arend
- Ruhr-Universität Bochum, Faculty of Biology and Biotechnology, AG Geobotany, Bochum, Germany
| | - Dominik Begerow
- Ruhr-Universität Bochum, Faculty of Biology and Biotechnology, AG Geobotany, Bochum, Germany
| | - Derek Peršoh
- Ruhr-Universität Bochum, Faculty of Biology and Biotechnology, AG Geobotany, Bochum, Germany.
| |
Collapse
|
10
|
Welzel M, Lange A, Heider D, Schwarz M, Freisleben B, Jensen M, Boenigk J, Beisser D. Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads. BMC Bioinformatics 2020; 21:526. [PMID: 33198651 PMCID: PMC7667751 DOI: 10.1186/s12859-020-03852-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 10/30/2020] [Indexed: 01/04/2023] Open
Abstract
Background Sequencing of marker genes amplified from environmental samples, known as amplicon sequencing, allows us to resolve some of the hidden diversity and elucidate evolutionary relationships and ecological processes among complex microbial communities. The analysis of large numbers of samples at high sequencing depths generated by high throughput sequencing technologies requires efficient, flexible, and reproducible bioinformatics pipelines. Only a few existing workflows can be run in a user-friendly, scalable, and reproducible manner on different computing devices using an efficient workflow management system. Results We present Natrix, an open-source bioinformatics workflow for preprocessing raw amplicon sequencing data. The workflow contains all analysis steps from quality assessment, read assembly, dereplication, chimera detection, split-sample merging, sequence representative assignment (OTUs or ASVs) to the taxonomic assignment of sequence representatives. The workflow is written using Snakemake, a workflow management engine for developing data analysis workflows. In addition, Conda is used for version control. Thus, Snakemake ensures reproducibility and Conda offers version control of the utilized programs. The encapsulation of rules and their dependencies support hassle-free sharing of rules between workflows and easy adaptation and extension of existing workflows. Natrix is freely available on GitHub (https://github.com/MW55/Natrix) or as a Docker container on DockerHub (https://hub.docker.com/r/mw55/natrix). Conclusion Natrix is a user-friendly and highly extensible workflow for processing Illumina amplicon data.
Collapse
Affiliation(s)
- Marius Welzel
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Anja Lange
- Department of Bioinformatics and Computational Biophysics, University of Duisburg-Essen, Essen, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Michael Schwarz
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Bernd Freisleben
- Department of Mathematics and Computer Science, University of Marburg, Marburg, Germany
| | - Manfred Jensen
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany
| | - Daniela Beisser
- Department of Biodiversity, University of Duisburg-Essen, Essen, Germany.
| |
Collapse
|
11
|
Juvigny-Khenafou NPD, Zhang Y, Piggott JJ, Atkinson D, Matthaei CD, Van Bael SA, Wu N. Anthropogenic stressors affect fungal more than bacterial communities in decaying leaf litter: A stream mesocosm experiment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:135053. [PMID: 31859062 DOI: 10.1016/j.scitotenv.2019.135053] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 06/10/2023]
Abstract
Despite the progress made in environmental microbiology techniques and knowledge, the succession and functional changes of the microbial community under multiple stressors are still poorly understood. This is a substantial knowledge gap as microbial communities regulate the biogeochemistry of stream ecosystems. Our study assessed the structural and temporal changes in stream fungal and bacterial communities associated with decomposing leaf litter under a multiple-stressor scenario. We conducted a fully crossed 4-factor experiment in 64 flow-through mesocosms fed by a pristine montane stream (21 days of colonisation, 21 days of manipulations) and investigated the effects of nutrient enrichment, flow velocity reduction and sedimentation after 2 and 3 weeks of stressor exposure. We used high-throughput sequencing and metabarcoding techniques (16S and 18S rRNA genes) to identify changes in microbial community composition. Our results indicate that (1) shifts in relative abundances of the pre-existing terrestrial microbial community, rather than changes in community identity, drove the observed responses to stressors; (2) changes in relative abundances within the microbial community paralleled decomposition rate patterns with time; (3) both fungal and bacterial communities had a certain resistance to stressors, as indicated by relatively minor changes in alpha diversity or multivariate community structure; (4) overall, stressor interactions were more common than stressor main effects when affecting microbial diversity metrics or abundant individual genera; and (5) stressor effects on microbes often changed from 2 weeks to 3 weeks of stressor exposure, with several response patterns being reversed. Our study suggests that future research should focus more on understanding the temporal dynamics of fungal and bacterial communities and how they relate to ecosystem processes to advance our understanding of the mechanisms associated with multiple-stressor interactions.
Collapse
Affiliation(s)
- Noël P D Juvigny-Khenafou
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK; Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| | - Yixin Zhang
- Department of Landscape Architecture, Gold Mantis School of Architecture, Soochow University, Suzhou, China.
| | - Jeremy J Piggott
- Trinity Centre for the Environment & Department of Zoology, School of Natural Sciences, Trinity College Dublin, The University of Dublin, College Green, Dublin 2, Ireland
| | - David Atkinson
- Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK
| | - Christoph D Matthaei
- Department of Zoology, University of Otago, PO Box 56, Dunedin 9054, New Zealand
| | - Sunshine A Van Bael
- Department of Ecology and Evolutionary Biology, Tulane University, 6823 St. Charles Avenue, Boggs 400, New Orleans, LA 70118, USA
| | - Naicheng Wu
- Department of Health and Environmental Science, Xi'an Jiaotong-Liverpool University, Suzhou, Jiangsu 215123, China
| |
Collapse
|
12
|
Inferences of environmental and biotic effects on patterns of eukaryotic alpha and beta diversity for the spring systems of Ash Meadows, Nevada. Oecologia 2019; 191:931-944. [PMID: 31628545 DOI: 10.1007/s00442-019-04526-6] [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: 07/07/2018] [Accepted: 10/09/2019] [Indexed: 10/25/2022]
Abstract
Freshwater springs are important ecosystems. In the arid regions of North America, groundwater extraction has caused the desiccation of springs and the extinction of taxa. To better describe the biodiversity of freshwater springs in the hope of establishing a sensitive approach for monitoring the predicted change in spring systems, we used high-resolution genetic methods to estimate the alpha and beta diversity of 19 springs and two reservoirs within the Ash Meadows National Wildlife Refuge in southwestern Nevada. We discovered a large number of distinct taxa based on eukaryote ribosomal gene sequences and show water temperature, spring size, and the presence or absence of non-native predators predicts alpha diversity, and temperature predicts beta diversity. Our study highlights how DNA data support inferences of environmental factors influencing community diversity and demonstrates the method may be an important tool for monitoring ecological communities.
Collapse
|
13
|
Nuy JK, Lange A, Beermann AJ, Jensen M, Elbrecht V, Röhl O, Peršoh D, Begerow D, Leese F, Boenigk J. Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 633:1287-1301. [PMID: 29758882 DOI: 10.1016/j.scitotenv.2018.03.077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 03/07/2018] [Accepted: 03/07/2018] [Indexed: 06/08/2023]
Abstract
Stream ecosystems are affected by multiple anthropogenic stressors worldwide. Even though effects of many single stressors are comparatively well studied, the effects of multiple stressors are difficult to predict. In particular bacteria and protists, which are responsible for the majority of ecosystem respiration and element flows, are infrequently studied with respect to multiple stressors responses. We conducted a stream mesocosm experiment to characterize the responses of single and multiple stressors on microbiota. Two functionally important stream habitats, leaf litter and benthic phototrophic rock biofilms, were exposed to three stressors in a full factorial design: fine sediment deposition, increased chloride concentration (salinization) and reduced flow velocity. We analyzed the microbial composition in the two habitat types of the mesocosms using an amplicon sequencing approach. Community analysis on different taxonomic levels as well as principle component analyses (PCoAs) based on realtive abundances of operational taxonomic units (OTUs) showed treatment specific shifts in the eukaryotic biofilm community. Analysis of variance (ANOVA) revealed that Bacillariophyta responded positively salinity and sediment increase, while the relative read abundance of chlorophyte taxa decreased. The combined effects of multiple stressors were mainly antagonistic. Therefore, the community composition in multiply stressed environments resembled the composition of the unstressed control community in terms of OTU occurrence and relative abundances.
Collapse
Affiliation(s)
- Julia K Nuy
- Department of Biodiversity, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Anja Lange
- Department of Bioinformatics and Computational Biophysics, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Arne J Beermann
- Aquatic Ecosystem Research, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Manfred Jensen
- Department of Biodiversity, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Vasco Elbrecht
- Aquatic Ecosystem Research, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Oliver Röhl
- Department of Geobotany, Ruhr - Universitaet Bochum, Universitaetsstraße. 150, D-44801 Bochum, Germany
| | - Derek Peršoh
- Department of Geobotany, Ruhr - Universitaet Bochum, Universitaetsstraße. 150, D-44801 Bochum, Germany
| | - Dominik Begerow
- Department of Geobotany, Ruhr - Universitaet Bochum, Universitaetsstraße. 150, D-44801 Bochum, Germany
| | - Florian Leese
- Aquatic Ecosystem Research, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg - Essen, Universitaetsstraße 5, D-45141 Essen, Germany.
| |
Collapse
|
14
|
Fungal guilds are evenly distributed along a vertical spruce forest soil profile while individual fungi show pronounced niche partitioning. Mycol Prog 2018. [DOI: 10.1007/s11557-018-1405-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
|
15
|
König J, Guerreiro MA, Peršoh D, Begerow D, Krauss J. Knowing your neighbourhood-the effects of Epichloë endophytes on foliar fungal assemblages in perennial ryegrass in dependence of season and land-use intensity. PeerJ 2018; 6:e4660. [PMID: 29780665 PMCID: PMC5958879 DOI: 10.7717/peerj.4660] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Accepted: 04/02/2018] [Indexed: 12/21/2022] Open
Abstract
Epichloë endophytes associated with cool-season grass species can protect their hosts from herbivory and can suppress mycorrhizal colonization of the hosts' roots. However, little is known about whether or not Epichloë endophyte infection can also change the foliar fungal assemblages of the host. We tested 52 grassland study sites along a land-use intensity gradient in three study regions over two seasons (spring vs. summer) to determine whether Epichloë infection of the host grass Lolium perenne changes the fungal community structure in leaves. Foliar fungal communities were assessed by Next Generation Sequencing of the ITS rRNA gene region. Fungal community structure was strongly affected by study region and season in our study, while land-use intensity and infection with Epichloë endophytes had no significant effects. We conclude that effects on non-systemic endophytes resulting from land use practices and Epichloë infection reported in other studies were masked by local and seasonal variability in this study's grassland sites.
Collapse
Affiliation(s)
- Julia König
- Department of Animal Ecology and Tropical Biology, Biocentre, University of Würzburg, Würzburg, Germany
| | | | - Derek Peršoh
- Department of Geobotany, Ruhr-Universität Bochum, Bochum, Germany
| | - Dominik Begerow
- Department of Geobotany, Ruhr-Universität Bochum, Bochum, Germany
| | - Jochen Krauss
- Department of Animal Ecology and Tropical Biology, Biocentre, University of Würzburg, Würzburg, Germany
| |
Collapse
|
16
|
Röhl O, Graupner N, Peršoh D, Kemler M, Mittelbach M, Boenigk J, Begerow D. Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities. MICROBIAL ECOLOGY 2018; 75:875-887. [PMID: 29026984 DOI: 10.1007/s00248-017-1085-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/29/2017] [Indexed: 05/22/2023]
Abstract
The increasing number and duration of inundations is reported to be a consequence of climate change and may severely compromise non-adapted macroorganisms. The effect of flooding events on terrestrial and aquatic microbial communities is, however, less well understood. They may respond to the changed abiotic properties of their native habitat, and the native community may change due to the introduction of alien species. We designed an experiment to investigate the effect of five different flooding durations on the terrestrial and aquatic communities of eukaryotic microorganism, using the AquaFlow mesocosms. With amplicon sequencing of the small subunit (SSU) and internal transcribed spacer (ITS) rRNA gene regions, we analyzed community compositions directly before and after flooding. Subsequently, they were monitored for another 28 days, to determine the sustainability of community changes. Our results revealed a temporary increase in similarity between terrestrial and aquatic communities according to OTU composition (operational taxonomic unit, serves as a proxy for species). Increased similarity was mainly caused by the transmission of OTUs from water to soil. A minority of these were able to persist in soil until the end of the experiment. By contrast, the vast majority of soil OTUs was not transmitted to water. Flooding duration affected the community structure (abundance) more than composition (occurrence). Terrestrial communities responded immediately to flooding and the flooding duration influenced the community changes. Independent from flooding duration, all terrestrial communities recovered largely after flooding, indicating a remarkable resilience to the applied disturbances. Aquatic communities responded immediately to the applied inundations too. At the end of the experiment, they grouped according to the applied flooding duration and the amount of ammonium and chloride that leached from the soil. This indicates a sustained long-term response of the aquatic communities to flooding events.
Collapse
Affiliation(s)
- Oliver Röhl
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany.
| | - Nadine Graupner
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Derek Peršoh
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Martin Kemler
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| | - Moritz Mittelbach
- AG Ökologie der Pflanzen; Institute of Biology, Freie Universität Berlin, Altensteinstr. 6, 14195, Berlin, Germany
| | - Jens Boenigk
- Department of Biodiversity, Faculty of Biology, University of Duisburg-Essen, Universitätsstr. 5, 45141, Essen, Germany
| | - Dominik Begerow
- AG Geobotany, Faculty of Biology and Biotechnology, Ruhr Universität Bochum, Universitätsstr. 150, 44801, Bochum, Germany
| |
Collapse
|
17
|
|