25
views
0
recommends
+1 Recommend
1 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Rainfall as a trigger of ecological cascade effects in an Australian groundwater ecosystem

      research-article

      Read this article at

          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Groundwaters host vital resources playing a key role in the near future. Subterranean fauna and microbes are crucial in regulating organic cycles in environments characterized by low energy and scarce carbon availability. However, our knowledge about the functioning of groundwater ecosystems is limited, despite being increasingly exposed to anthropic impacts and climate change-related processes. In this work we apply novel biochemical and genetic techniques to investigate the ecological dynamics of an Australian calcrete under two contrasting rainfall periods (LR—low rainfall and HR—high rainfall). Our results indicate that the microbial gut community of copepods and amphipods experienced a shift in taxonomic diversity and predicted organic functional metabolic pathways during HR. The HR regime triggered a cascade effect driven by microbes (OM processors) and exploited by copepods and amphipods (primary and secondary consumers), which was finally transferred to the aquatic beetles (top predators). Our findings highlight that rainfall triggers ecological shifts towards more deterministic dynamics, revealing a complex web of interactions in seemingly simple environmental settings. Here we show how a combined isotopic-molecular approach can untangle the mechanisms shaping a calcrete community. This design will help manage and preserve one of the most vital but underrated ecosystems worldwide.

          Related collections

          Most cited references69

          • Record: found
          • Abstract: found
          • Article: not found

          Basic local alignment search tool.

          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

            Background The analysis of microbial communities through DNA sequencing brings many challenges: the integration of different types of data with methods from ecology, genetics, phylogenetics, multivariate statistics, visualization and testing. With the increased breadth of experimental designs now being pursued, project-specific statistical analyses are often needed, and these analyses are often difficult (or impossible) for peer researchers to independently reproduce. The vast majority of the requisite tools for performing these analyses reproducibly are already implemented in R and its extensions (packages), but with limited support for high throughput microbiome census data. Results Here we describe a software project, phyloseq, dedicated to the object-oriented representation and analysis of microbiome census data in R. It supports importing data from a variety of common formats, as well as many analysis techniques. These include calibration, filtering, subsetting, agglomeration, multi-table comparisons, diversity analysis, parallelized Fast UniFrac, ordination methods, and production of publication-quality graphics; all in a manner that is easy to document, share, and modify. We show how to apply functions from other R packages to phyloseq-represented data, illustrating the availability of a large number of open source analysis techniques. We discuss the use of phyloseq with tools for reproducible research, a practice common in other fields but still rare in the analysis of highly parallel microbiome census data. We have made available all of the materials necessary to completely reproduce the analysis and figures included in this article, an example of best practices for reproducible research. Conclusions The phyloseq project for R is a new open-source software package, freely available on the web from both GitHub and Bioconductor.
              • Record: found
              • Abstract: found
              • Article: not found

              Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample.

              The ongoing revolution in high-throughput sequencing continues to democratize the ability of small groups of investigators to map the microbial component of the biosphere. In particular, the coevolution of new sequencing platforms and new software tools allows data acquisition and analysis on an unprecedented scale. Here we report the next stage in this coevolutionary arms race, using the Illumina GAIIx platform to sequence a diverse array of 25 environmental samples and three known "mock communities" at a depth averaging 3.1 million reads per sample. We demonstrate excellent consistency in taxonomic recovery and recapture diversity patterns that were previously reported on the basis of metaanalysis of many studies from the literature (notably, the saline/nonsaline split in environmental samples and the split between host-associated and free-living communities). We also demonstrate that 2,000 Illumina single-end reads are sufficient to recapture the same relationships among samples that we observe with the full dataset. The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution.

                Author and article information

                Contributors
                mattia.sacco@curtin.edu.au
                Journal
                Sci Rep
                Sci Rep
                Scientific Reports
                Nature Publishing Group UK (London )
                2045-2322
                12 February 2021
                12 February 2021
                2021
                : 11
                : 3694
                Affiliations
                [1 ]GRID grid.1032.0, ISNI 0000 0004 0375 4078, WA-Organic Isotope Geochemistry Centre, The Institute for Geoscience Research, School of Earth and Planetary Sciences, , Curtin University, ; Perth, WA 6102 Australia
                [2 ]GRID grid.1032.0, ISNI 0000 0004 0375 4078, Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, , Curtin University, ; Perth, WA 6102 Australia
                [3 ]GRID grid.1032.0, ISNI 0000 0004 0375 4078, School of Molecular and Life Sciences, , Curtin University, ; Perth, WA 6102 Australia
                [4 ]GRID grid.452917.c, ISNI 0000 0000 9848 8286, Collections and Research Centre, , Western Australian Museum, ; Welshpool, WA 6986 Australia
                [5 ]GRID grid.1012.2, ISNI 0000 0004 1936 7910, School of Biological Sciences, , University of Western Australia, ; Crawley, WA 6009 Australia
                [6 ]GRID grid.1010.0, ISNI 0000 0004 1936 7304, Australian Centre for Evolutionary Biology and Biodiversity, School of Biological Sciences, , University of Adelaide, ; Adelaide, SA 5005 Australia
                [7 ]GRID grid.437963.c, ISNI 0000 0001 1349 5098, Evolutionary Biology Unit, , South Australian Museum, North Terrace, ; Adelaide, SA 5000 Australia
                [8 ]GRID grid.1089.0, ISNI 0000 0004 0432 8812, Australian Nuclear Science and Technology Organisation (ANSTO), ; Locked Bag 2001, Kirrawee DC, NSW 2232 Australia
                [9 ]GRID grid.1018.8, ISNI 0000 0001 2342 0938, Department of Archaeology and History, , La Trobe University, ; Bundoora, VIC 3086 Australia
                [10 ]GRID grid.23520.36, ISNI 0000 0000 8569 1592, Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, , Universidad de Burgos, ; 09001 Burgos, Spain
                [11 ]GRID grid.10420.37, ISNI 0000 0001 2286 1424, Department of Functional and Evolutionary Ecology, , University of Vienna, ; 1090 Vienna, Austria
                Article
                83286
                10.1038/s41598-021-83286-x
                7881013
                33580159
                7e099857-b6ce-4e5e-914e-e7f0f5bc5a6a
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 10 September 2020
                : 27 January 2021
                Funding
                Funded by: Australian Research Council
                Award ID: LP140100555
                Funded by: FundRef http://dx.doi.org/10.13039/501100001797, Curtin University of Technology;
                Award ID: Curtin International Postgraduate Research Scholarship
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100001023, Australian Institute of Nuclear Science and Engineering;
                Award ID: AINSE postgraduate scholarship
                Award Recipient :
                Categories
                Article
                Custom metadata
                © The Author(s) 2021

                Uncategorized
                biochemistry,ecology,biogeochemistry,ecosystem ecology,freshwater ecology,microbial ecology,stable isotope analysis

                Comments

                Comment on this article

                Related Documents Log