@prefix dcat: . @prefix dct: . @prefix foaf: . @prefix vcard: . @prefix xsd: . a dcat:Dataset ; dct:description """#Tranche 1: Project 1.3#\r \r ###In a New Zealand first, researchers have developed a nationwide database to integrate and share eDNA data to allow biological diversity across our diverse landscapes to be assessed and compared.###\r \r **Overview**\r \r The analysis of eDNA requires the extraction and identification of DNA directly from environmental samples such as soil or freshwater.\r \r Environmental DNA, or eDNA, refers to the DNA that is shed or excreted from biological organisms, for example as skin, hair, faeces or urine. It provides a window into the world of biological diversity that is otherwise largely hidden from view.\r \r This powerful technology is transforming how biological diversity is measured. It was used by a BioHeritage research team led by Dr Gavin Lear, University of Auckland, to develop a nationwide database – or virtual hub – that integrated eDNA data with existing monitoring programmes.\r \r **Project Leader**\r \r - Gavin Lear, University of Auckland\r """ ; dct:identifier "79c78f6a-ecea-4fd8-93bc-7a71989713ca" ; dct:issued "2024-06-26T02:45:30.458875"^^xsd:dateTime ; dct:modified "2024-07-31T03:06:39.656730"^^xsd:dateTime ; dct:publisher ; dct:title "eDNA For Environmental Monitoring" ; dcat:contactPoint [ a vcard:Organization ; vcard:fn "BioHeritage Support" ; vcard:hasEmail ] ; dcat:distribution , , , , , , , , , , , , , , , , , , , , , . a dcat:Distribution ; dct:description """###Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples###\r \r **January 2018**\r \r **Lear G, Dickie I, Banks J, Boyer S, Buckley HL, Buckley TR, Cruickshank R, Dopheide A, Handley KM, Hermans S, Kamke J, Lee CK, MacDiarmid R, Morales SE, Orlovich D, Smissen R, Wood J & Holdaway R. 2018. [Methods for the extraction, storage, amplification and sequencing of DNA from environmental samples](https://newzealandecology.org/nzje/3323.pdf). New Zealand Journal of Ecology 42(1): 10-+.**\r \r **ABSTRACT**\r \r Advances in the sequencing of DNA extracted from media such as soil and water offer huge opportunities for biodiversity monitoring and assessment, particularly where the collection or identification of whole organisms is impractical. However, there are myriad methods for the extraction, storage, amplification and sequencing of DNA from environmental samples. To help overcome potential biases that may impede the effective comparison of biodiversity data collected by different researchers, we propose a standardised set of procedures for use on different taxa and sample media, largely based on recent trends in their use.\r \r **KEYWORDS**\r \r biological heritage, biodiversity monitoring, community profiling, DNA primers, DNA sequencing, eDNA, environmental DNA, Illumina, metabarcoding, metagenomics, molecular ecology""" ; dct:issued "2024-07-05T04:30:49.731125"^^xsd:dateTime ; dct:modified "2024-07-05T04:30:49.731125"^^xsd:dateTime ; dct:title "PAPER: Extraction, storage, amplification and sequencing of environmental DNA" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Environmental DNA sampling detects between-habitat variation in soil arthropod communities, but is a poor indicator of fine-scale spatial and seasonal variation###\r \r **July 2022**\r \r **Hermans SM, Lear G, Buckley TR, Buckley HL 2022. [Environmental DNA sampling detects between-habitat variation in soil arthropod communities, but is a poor indicator of fine-scale spatial and seasonal variation](https://www.sciencedirect.com/science/article/pii/S1470160X22005118/pdfft?md5=d09e6ed96f4bd8ef90bf7f8b0582ff35&pid=1-s2.0-S1470160X22005118-main.pdf). Ecological Indicators 140: 109040.**\r \r **ABSTRACT**\r \r Arthropods have been useful and important ecological indicators of environmental change, but morphological identification of key groups is labour-intensive and expertise-demanding. Molecular methods using environmental DNA (eDNA) offer high-throughput capabilities for monitoring arthropod biodiversity, though their effectiveness in detecting biodiversity variation over space and time is unclear. This study employed a standard eDNA metabarcoding approach to monitor subterranean arthropod communities in a homogeneous (pine plantation) and a heterogeneous (regenerating native woody vegetation) forest.\r \r **KEYWORDS**\r \r Biodiversity monitoring; Environmental DNA; Arthropods; Soil invertebrates; Molecular methods; Metabarcoding; Cytochrome c oxidase I (COI)""" ; dct:issued "2024-07-03T05:04:47.769534"^^xsd:dateTime ; dct:modified "2024-07-03T05:04:47.769534"^^xsd:dateTime ; dct:title "PAPER: Environmental DNA sampling in soil arthropod communities" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Connecting through space and time: catchment-scale distributions of bacteria in soil, stream water and sediment###\r \r **August 2019**\r \r **Hermans SM, Buckley HL, Case BS, Lear G 2020. [Connecting through space and time: catchment-scale distributions of bacteria in soil, stream water and sediment](https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.14792). Environ Microbiol 22(3): 1000-1010.**\r \r **ABSTRACT**\r \r Terrestrial and aquatic environments are linked through hydrological networks that transport abiotic components from upslope environments into aquatic ecosystems. However, our understanding of how bacteria are transported through these same networks is limited. Here, we applied 16S rRNA gene sequencing to over 500 soil, stream water and stream sediment samples collected within a native forest catchment to determine the extent to which bacterial communities in these habitats are connected. We provide evidence that while the bacterial communities in each habitat were significantly distinct from one another (PERMANOVA pairwise P < 0.001), the bacterial communities in soil and stream samples were weakly connected to each other when stream sediment sample locations were downhill of surface runoff flow paths. This pattern decreased with increasing distance between the soil and sediment samples. The connectivity between soil and stream water samples was less apparent and extremely transient; the greatest similarity between bacterial communities in soil and stream water overall was when comparing stream samples collected 1 week post soil sampling. This study shows how bacterial communities in soil, stream water and stream sediments are connected at small spatial scales and provides rare insights into the temporal dynamics of terrestrial and aquatic bacterial community connectivity.\r \r **KEYWORDS**\r \r Bacteria; Bacterial Physiological Phenomena; Ecosystem; Forests; Geologic Sediments; RNA, Ribosomal, 16S; Rivers; Soil Microbiology; Water Microbiology""" ; dct:issued "2024-06-26T03:04:14.050614"^^xsd:dateTime ; dct:modified "2024-06-26T03:04:14.050614"^^xsd:dateTime ; dct:title "PAPER: Catchment-scale distributions of bacteria" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Using soil bacterial communities to predict physico-chemical variables and soil quality###\r \r **June 2020**\r \r **Hermans SM, Buckley HL, Case BS, Curran-Cournane F, Taylor M, Lear G 2020. [Using soil bacterial communities to predict physico-chemical variables and soil quality](https://microbiomejournal.biomedcentral.com/counter/pdf/10.1186/s40168-020-00858-1.pdf). Microbiome 8(1): 79**\r \r **ABSTRACT**\r \r Soil ecosystems consist of complex interactions between biological communities and physico-chemical variables, all of which contribute to the overall quality of soils. Despite this, changes in bacterial communities are ignored by most soil monitoring programs, which are crucial to ensure the sustainability of land management practices. We applied 16S rRNA gene sequencing to determine the bacterial community composition of over 3000 soil samples from 606 sites in New Zealand. Sites were classified as indigenous forests, exotic forest plantations, horticulture, or pastoral grasslands; soil physico-chemical variables related to soil quality were also collected. The composition of soil bacterial communities was then used to predict the land use and soil physico-chemical variables of each site.\r \r **KEYWORDS**\r \r Bacterial communities;\r Bacterial indicators;\r Biomonitoring;\r Environmental monitoring;\r Random forest analysis;\r Soil health;\r Soil microbiology;""" ; dct:issued "2024-07-01T02:20:54.705142"^^xsd:dateTime ; dct:modified "2024-07-01T02:20:54.705142"^^xsd:dateTime ; dct:title "PAPER: Predicting soil quality" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Towards robust and repeatable sampling methods in eDNA‐based studies###\r \r **May 2018**\r \r **Dickie IA, Boyer S, Buckley HL, Duncan RP, Gardner PP, Hogg ID, Holdaway RJ, Lear G, Makiola A, Morales SE, Powell JR & Weaver L. 2018. [Towards robust and repeatable sampling methods in eDNA-based studies](https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.12907). Mol Ecol Resour.**\r \r **ABSTRACT**\r \r DNA-based techniques are increasingly used for measuring the biodiversity (species presence, identity, abundance and community composition) of terrestrial and aquatic ecosystems. While there are numerous reviews of molecular methods and bioinformatic steps, there has been little consideration of the methods used to collect samples upon which these later steps are based. This represents a critical knowledge gap, as methodologically sound field sampling is the foundation for subsequent analyses. Were viewed field sampling methods used for metabarcoding studies of both terrestrial and freshwater ecosystem biodiversity over a nearly three-year period (n=75). We found that 95% (n=71) of these studies used subjective sampling methods and in appropriate field methods and/or failed to provide critical methodological information. It would be possible for researchers to replicate only 5% of the metabarcoding studies in our sample, a poorer level of reproducibility than for ecological studies in general. Our findings suggest greater attention to field sampling methods, and reporting is necessary in eDNA-based studies of biodiversity to ensure robust outcomes and future reproducibility. Methods must be fully and accurately reported, and protocols developed that minimize subjectivity. Standardization of sampling protocols would be one way to help to improve reproducibility and have additional benefits in allowing compilation and comparison of data from across studies.\r \r **KEYWORDS**\r \r contamination; environmental DNA; experimental design; metabarcoding; metadata; sampling""" ; dct:issued "2024-07-05T04:22:01.345485"^^xsd:dateTime ; dct:modified "2024-07-05T04:22:01.345485"^^xsd:dateTime ; dct:title "PAPER Robust and repeatable sampling for eDNA‐based studies" ; dcat:accessURL . a dcat:Distribution ; dct:description """###A Systematic Review of Sources of Variability and Uncertainty in eDNA Data for Environmental Monitoring###\r \r **May 2020**\r \r **Mathieu C, Hermans SM, Lear G, Buckley TR, Lee KVC, Buckley HL 2020. [A Systematic Review of Sources of Variability and Uncertainty in eDNA Data for Environmental Monitoring](https://www.frontiersin.org/journals/ecology-and-evolution/articles/10.3389/fevo.2020.00135/pdf?isPublishedV2=false). Frontiers in Ecology and Evolution 8(135).**\r \r **ABSTRACT**\r \r Environmental DNA (eDNA) is becoming a standard tool in environmental monitoring that aims to quantify spatiotemporal variation for the measurement and prediction of ecosystem change. eDNA surveys have complex workflows encompassing multiple decision-making steps in which uncertainties can accumulate due to field sampling design, molecular biology lab work, and bioinformatics analyses.\r \r **KEYWORDS**\r \r bioinformatics;\r community;\r edna;\r experimental design;\r single taxon;\r spatiotemporal scale;\r uncertainty;\r variability;\r microbial ecology;\r occupancy models;\r DNA extraction;\r biodiversity;\r diversity;\r bacterial;\r communities;\r abundance;\r scale;\r sensitivity;\r """ ; dct:issued "2024-07-01T04:16:01.477923"^^xsd:dateTime ; dct:modified "2024-07-01T04:16:01.477923"^^xsd:dateTime ; dct:title "PAPER: Variability and Uncertainty in eDNA Data " ; dcat:accessURL . a dcat:Distribution ; dct:description """###Aspect has a greater impact on alpine soil bacterial community structure###\r \r **December 2016**\r \r **Wu J, Anderson BJ, Buckley HL, Lewis G, Lear G 2017. [Aspect has a greater impact on alpine soil bacterial community structure than elevation](https://academic.oup.com/femsec/article-pdf/93/3/fiw253/16737485/fiw253.pdf). FEMS Microbiol Ecol 93(3).**\r \r **ABSTRACT**\r \r Gradients in environmental conditions, including climate factors and resource availability, occur along mountain inclines, providing a ‘natural laboratory’ to explore their combined impacts on microbial distributions. Conflicting spatial patterns observed across elevation gradients in soil bacterial community structure suggest that they are driven by various interacting factors at different spatial scales. Here, we investigated the relative impacts of non-resource (e.g. soil temperature, pH) and resource conditions (e.g. soil carbon and nitrogen) on the biogeography of soil bacterial communities across broad (i.e. along a 1500 m mountain elevation gradient) and fine sampling scales (i.e. along sunny and shady aspects of a mountain ridge). Our analysis of 16S rRNA gene data confirmed that when sampling across distances of < 1000 m, bacterial community composition was more closely related to the aspect of a site than its elevation. However, despite large differences in climate and resource-availability factors across elevation- and aspect-related gradients, bacterial community composition and richness were most strongly correlated with soil pH. These findings highlight the need to incorporate knowledge of multiple factors, including site aspect and soil pH for the appropriate use of elevation gradients as a proxy to explore the impacts of climate change on microbial community composition.\r \r **KEYWORDS**\r \r 16S rRNA; next-generation sequencing; micro-climate; soil microbiology; pH gradient\r """ ; dct:issued "2024-06-26T04:01:35.295204"^^xsd:dateTime ; dct:modified "2024-06-26T04:01:35.295204"^^xsd:dateTime ; dct:title "PAPER: Soil bacteria community structure" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Polygenic basis for adaptive morphological variation in a threatened Aotearoa New Zealand bird, the hihi (*Notiomystis cincta*)###\r \r **August 2020**\r \r **Duntsch L, Tomotani BM, de Villemereuil P, Brekke P, Lee KD, Ewen JG, and Santure AW 2020. [Polygenic basis for adaptive morphological variation in a threatened Aotearoa New Zealand bird, the hihi (*Notiomystis cincta*)](https://royalsocietypublishing.org/doi/epdf/10.1098/rspb.2020.0948). Proc Biol Sci 287(1933): 20200948.**\r \r **ABSTRACT**\r \r To predict if a threatened species can adapt to changing selective pressures, it is crucial to understand the genetic basis of adaptive traits, especially in species historically affected by severe bottlenecks. In this research, genomic data was used to reveal previously undiscovered genetic patterns underlying three adaptive morphological phenotypes in the Tiritiri Matangi population of the threatened Aotearoa New Zealand bird, the hihi (*Notiomystis cincta*). \r \r **KEYWORDS**\r \r genomic relatedness matrix; chromosome partitioning; genome-wide association; polygenic traits; pedigree study; *Notiomystis cincta*\r """ ; dct:issued "2024-07-03T04:29:00.252845"^^xsd:dateTime ; dct:modified "2024-07-03T04:29:00.252845"^^xsd:dateTime ; dct:title "PAPER: Polygenic basis for morphological variation" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data###\r \r **June 2021**\r \r **Lewe N, Hermans S, Lear G, Kelly LT, Thomson-Laing G, Weisbrod B, Wood SA, Keyzers RA, Deslippe JR 2021. [Phospholipid fatty acid (PLFA) analysis as a tool to estimate absolute abundances from compositional 16S rRNA bacterial metabarcoding data.](https://www.sciencedirect.com/science/article/pii/S0167701221001391/pdfft?md5=18a7f1d07553bc4afbc70fa960eff592&pid=1-s2.0-S0167701221001391-main.pdf) J Microbiol Methods 188: 106271.**\r \r **ABSTRACT**\r \r Microbial biodiversity monitoring through the analysis of DNA extracted from environmental samples is increasingly popular because it is perceived as being rapid, cost-effective, and flexible concerning the sample types studied. DNA can be extracted from diverse media before high-throughput sequencing of the prokaryotic 16S rRNA gene is used to characterize the taxonomic diversity and composition of the sample (known as metabarcoding). While sources of bias in metabarcoding methodologies are widely acknowledged, previous studies have focused mainly on the effects of these biases within a single substrate type, and relatively little is known of how these vary across substrates. We investigated the effect of substrate type (water, microbial mats, lake sediments, stream sediments, soil and a mock microbial community) on the relative performance of DNA metabarcoding in parallel with phospholipid fatty acid (PLFA) analysis. \r \r **KEYWORDS**\r \r eDNA; Microbial biomass; PLFA; Environmental monitoring; Biomarker; Environmental substrates\r """ ; dct:issued "2024-07-03T04:11:00.046033"^^xsd:dateTime ; dct:modified "2024-07-03T04:11:00.046033"^^xsd:dateTime ; dct:title "PAPER: Phospholipid fatty acid analysis as a tool " ; dcat:accessURL . a dcat:Distribution ; dct:description """###DNA metabarcoding of prey reveals spatial, temporal and diet partitioning of an island ecosystem by four invasive wasps###\r \r **March 2021**\r \r **Schmack JM, Lear G, Astudillo-Garcia C, Boyer S, Ward DF, Beggs JR 2021. [DNA metabarcoding of prey reveals spatial, temporal and diet partitioning of an island ecosystem by four invasive wasps](https://besjournals.onlinelibrary.wiley.com/doi/epdf/10.1111/1365-2664.13856). Journal of Applied Ecology 58(6): 1199-1211.**\r \r **ABSTRACT**\r \r Invasive alien species can cause detrimental changes in native ecosystems, but our understanding of the interactions between multiple exotic species is limited. To evaluate the joint effect of multiple sympatric invaders on an ecosystem, we must first understand how they interact with each other.\r \r Here, we quantified the spatial distribution, dietary composition and overlap of four invasive generalist vespid species (two *Vespula* and two *Polistes*) that co-occur on Ahuahu off the north-east coast of New Zealand. We used DNA metabarcoding of larval faecal material to identify prey species, and mapped the locations of nests.\r \r **KEYWORDS**\r \r diet overlap; environmental DNA; invasive species; *Lepidoptera*; niche partitioning; *Polistes*; resource competition; *Vespula*\r """ ; dct:issued "2024-07-03T04:46:05.342570"^^xsd:dateTime ; dct:modified "2024-07-03T04:46:05.342570"^^xsd:dateTime ; dct:title "PAPER: DNA metabarcoding of invasive wasp prey" ; dcat:accessURL . a dcat:Distribution ; dct:description """###DNA metabarcoding as a tool for invertebrate community monitoring: a case study comparison with conventional techniques###\r \r **January 2019**\r \r **Watts C, Dopheide A, Holdaway R, Davis C, Wood J, Thornburrow D, Dickie IA 2019. [DNA metabarcoding as a tool for invertebrate community monitoring: a case study comparison with conventional techniques.](https://onlinelibrary.wiley.com/doi/epdf/10.1111/aen.12384) Austral Entomology 58(3): 675-686.**\r \r **ABSTRACT**\r \r When conserving native biodiversity, it is particularly important to consider invertebrates, a diverse and functionally important component of biodiversity. However, their inclusion in monitoring and conservation planning has lagged behind larger fauna because collecting, sorting and identifying invertebrates using conventional monitoring techniques is often expensive, time consuming and restricted by expertise in diagnostics. Emerging DNA metabarcoding techniques could potentially revolutionise monitoring of invertebrates by providing the ability to characterise entire communities from a single, easily collected environmental sample. We aimed to characterise the invertebrate fauna of an isolated, coastal forest fragment in New Zealand using the same level of financial investment for conventional invertebrate monitoring (pitfall and malaise traps) and a DNA metabarcoding approach applied to two alternative sample types (conventional invertebrate samples and soil samples). The bulk invertebrate and soil DNA metabarcoding methods were able to reproduce ecological patterns observed in the beetle community detected using conventional sampling. The soil DNA metabarcoding method detected a different beetle community and a more diverse array of invertebrate taxa than conventional sampling techniques. DNA metabarcoding offers conservation managers a practical, cost-effective technique for characterising whole invertebrate communities. However, increasing the taxonomic coverage of reference sequence databases (particularly for New Zealand invertebrates) through DNA barcoding efforts should be the focus of future research as it would improve the utility of metabarcoding methods for invertebrate monitoring, which would complement conventional techniques.\r \r **KEYWORDS**\r \r coi;\r edge effect;\r environmental DNA;\r forest;\r biodiversity;\r bioindicators;\r sequences;\r responses;""" ; dct:issued "2024-06-26T02:52:28.614969"^^xsd:dateTime ; dct:modified "2024-06-26T02:52:28.614969"^^xsd:dateTime ; dct:title "PAPER: DNA metabarcoding as a tool for monitoring" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Following Rapoport's Rule: the geographic range and genome size of bacterial taxa decline at warmer latitudes###\r \r **May 2016**\r \r **Lear G, Lau K, Perchec AM, Buckley HL, Case BS, Neale M, Fierer N, Leff JW, Handley KM, Lewis G 2017. [Following Rapoport's Rule: the geographic range and genome size of bacterial taxa decline at warmer latitudes](https://enviromicro-journals.onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.13797). Environ Microbiol 19(8): 3152-3162.**\r \r **ABSTRACT**\r \r We sought to test whether stream bacterial communities conform to Rapoport’s Rule, a pattern commonly observed for plants and animals whereby taxa exhibit decreased latitudinal range sizes closer to the equator. Using a DNA sequencing approach, we explored the biogeography of biofilm bacterial communities in 204 streams across a ∼1000 km latitudinal gradient. The range sizes of bacterial taxa were strongly correlated with latitude, decreasing closer to the equator, which coincided with a greater than fivefold increase in bacterial taxonomic richness. The relative richness and range size of bacteria were associated with spatially correlated variation in temperature and rainfall. These patterns were observed despite enormous variability in catchment environmental characteristics. Similar results were obtained when restricting the same analyses to native forest catchments, thereby controlling for spatial biases in land use. We analysed genomic data from ∼500 taxa detected in this study, for which data were available and found that bacterial communities at cooler latitudes also tended to possess greater potential metabolic potential. Collectively, these data provide the first evidence of latitudinal variation in the range size distributions of freshwater bacteria, a trend which may be determined, in part, by a trade-off between bacterial genome size and local variation in climatic conditions.\r \r **KEYWORDS**\r \r Altitude; Bacteria; Biodiversity; Biofilms; Genome size; Genome, Bacterial; Phylogeny; Rivers; Latitudinal gradient; Metabolic potential; Geographic range""" ; dct:issued "2024-06-26T04:12:48.052049"^^xsd:dateTime ; dct:modified "2024-06-26T04:12:48.052049"^^xsd:dateTime ; dct:title "PAPER: Following Rapoport's Rule" ; dcat:accessURL . a dcat:Distribution ; dct:description """###A comparison of the ability of PLFA and 16S rRNA gene metabarcoding to resolve soil community change and predict ecosystem functions###\r \r **February 2018**\r \r **Orwin KH, Dickie IA, Holdaway R, Wood JR 2018. [A comparison of the ability of PLFA and 16S rRNA gene metabarcoding to resolve soil community change and predict ecosystem functions](https://www.sciencedirect.com/science/article/pii/S0038071717306363/pdfft?md5=ab41c6bb6a13ca73e27a572a9f80ee56&pid=1-s2.0-S0038071717306363-main.pdf). Soil Biology & Biochemistry 117: 27-35.**\r \r **ABSTRACT**\r \r Soil bacterial community structure has traditionally been measured using phospholipid fatty acid (PLFA) profiling. However, with the development of high-throughput sequencing technologies and metabarcoding techniques, more studies are now using 16S rRNA gene metabarcoding to measure bacterial community structure. Metabarcoding provides a much greater level of detail than PLFA profiling does, but it remains unclear whether or not the two techniques have a similar ability to answer many of the common questions asked by ecologists. We test the relative ability of the two techniques to quantify differences in bacterial community structure among five land uses (natural and planted forest, unimproved and improved grasslands, and vineyards), and to predict ecosystem functions. We also test whether PLFA- and metabarcoding-based metrics indicative of microbial growth strategies are correlated to each other. We show that both techniques showed broadly similar patterns of bacterial community composition change with land use and a remarkably similar ability to predict a wide range of ecosystem functions (carbon and nutrient cycling, and responses to drought). However, they were also complementary, as each showed different strengths in discriminating land uses and predicting ecosystem functions. PLFA metrics (i.e. the gram-positive:gram-negative ratio and fungal:bacterial ratio) were strongly correlated with the equivalent 16S rRNA gene metabarcoding metrics (i.e. the gram-positive:gram-negative and oligotrophic:copiotrophic ratios), although PLFA metrics were less well correlated with the Proteobacteria:Acidobacteria ratio. For many ecological questions the two techniques thus give broadly comparable results, providing confidence in the ability of both techniques to quantify meaningful changes in bacterial communities.\r \r **KEYWORDS**\r \r PLFA; 16S rRNA gene metabarcoding; Land use; Carbon cycling; Nutrient cycling; Stability""" ; dct:issued "2024-07-05T03:36:22.514126"^^xsd:dateTime ; dct:modified "2024-07-05T03:36:22.514126"^^xsd:dateTime ; dct:title "PAPER: Comparison of PLFA and 16S rRNA gene metabarcoding" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Temporal variation in soil bacterial communities can be confounded with spatial variation###\r \r **September 2020**\r \r **Hermans SM, Buckley HL, Curran-Cournane F, Taylor M, Lear G. 2020. [Temporal variation in soil bacterial communities can be confounded with spatial variation.](https://academic.oup.com/femsec/article-pdf/96/12/fiaa192/34548805/fiaa192.pdf) FEMS Microbiol Ecol 96(12).**\r \r \r **ABSTRACT**\r \r Investigating temporal variation in soil bacterial communities advances our fundamental understanding of the causal processes driving biological variation, and how the composition of these important ecosystem members may change into the future. Despite this, temporal variation in soil bacteria remains understudied, and the effects of spatial heterogeneity in bacterial communities on the detection of temporal changes is largely unknown. Using 16S rRNA gene amplicon sequencing, we evaluated temporal patterns in soil bacterial communities from indigenous forest and human-impacted sites sampled repeatedly over a 5-year period.\r \r **KEYWORDS**\r \r 16S rRNA; soil microbial ecology; spatial variation; temporal variation; native forests; primary forests; environmental monitoring; soil health\r """ ; dct:issued "2024-07-03T04:02:48.495683"^^xsd:dateTime ; dct:modified "2024-07-03T04:02:48.495683"^^xsd:dateTime ; dct:title "PAPER: Temporal variation in soil bacterial communities" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Bacteria as Emerging Indicators of Soil Condition###\r \r **December 2016**\r \r **Hermans SM, Buckley HL, Case BS, Curran-Cournane F, Taylor M, Lear G 2017. [Bacteria as Emerging Indicators of Soil Condition](https://journals.asm.org/doi/reader/10.1128/AEM.02826-16). Appl Environ Microbiol 83(1).**\r \r **ABSTRACT**\r \r Bacterial communities are important for the health and productivity of soil ecosystems and have great potential as novel indicators of environmental perturbations. To assess how they are affected by anthropogenic activity and to determine their ability to provide alternative metrics of environmental health, we sought to define which soil variables bacteria respond to across multiple soil types and land uses. \r \r **KEYWORDS**\r \r Bacteria; Biodiversity; Carbon; Climate; Ecosystem; Hydrogen-Ion Concentration; Microbial Consortia; Nitrogen; Phosphorus; Phylogeny; RNA, Ribosomal, 16S; Soil; Soil Microbiology""" ; dct:issued "2024-06-26T04:06:11.447741"^^xsd:dateTime ; dct:modified "2024-06-26T04:06:11.447741"^^xsd:dateTime ; dct:title "PAPER: Bacteria as Emerging Indicators of Soil Condition" ; dcat:accessURL . a dcat:Distribution ; dct:description """###From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential###\r \r **March 2020**\r \r **Hermans SM, Taylor M, Grelet G, Curran-Cournane F, Buckley HL, Handley KM, Lear G 2020. [From pine to pasture: land use history has long-term impacts on soil bacterial community composition and functional potential.]( https://academic.oup.com/femsec/article-pdf/96/4/fiaa041/33009812/fiaa041.pdf) FEMS Microbiol Ecol 96(4).**\r \r **ABSTRACT** \r \r Bacterial communities are crucial to soil ecosystems and are known to be sensitive to environmental changes. However, our understanding of how present-day soil bacterial communities remain impacted by historic land uses is limited; implications for their functional potential are especially understudied. Through 16S rRNA gene amplicon and shotgun metagenomic sequencing, we characterized the structure and functional potential of soil bacterial communities after land use conversion.\r \r **KEYWORDS**\r \r bacterial communities; metagenomics; land use; pine forest; dairy; pasture; functional diversity nitrogen cycle""" ; dct:issued "2024-07-03T02:53:50.346450"^^xsd:dateTime ; dct:modified "2024-07-03T02:53:50.346450"^^xsd:dateTime ; dct:title "PAPER: Land use history impact on soil bacteria " ; dcat:accessURL . a dcat:Distribution ; dct:description """###Using DNA metabarcoding to assess New Zealand's terrestrial biodiversity.###\r \r **May 2017**\r \r **Holdaway RJ, Wood JR, Dickie IA, Orwin KH, Bellingham PJ, Richardson SJ, Lyver PO, Timoti P, Buckley TR 2017. [Using DNA metabarcoding to assess New Zealand's terrestrial biodiversity.](https://newzealandecology.org/nzje/3310.pdf) New Zealand Journal of Ecology 41(2): 251-262.**\r \r **ABSTRACT**\r \r High throughput DNA sequencing technology has enabled entire biological communities to be characterised from DNA derived from pools of organisms, such as bulk-collected invertebrates, or DNA extracted from environmental samples (e.g. soil). These DNA-based techniques have the potential to revolutionise biodiversity monitoring. One approach in particular, DNA metabarcoding, can provide unprecedented taxonomic breadth at a scale not practically achievable through the morphological identification of individual organisms. Here, we assess the current strengths and weaknesses of DNA metabarcoding techniques for biodiversity assessment. We argue that it is essential to integrate conventional monitoring methods with novel DNA methods, to validate methods, and to better use and interpret data. We present a conceptual framework for how this might be done, explore potential applications within national biodiversity assessment frameworks, Māori biodiversity monitoring and the primary sector, and highlight areas of current uncertainty and future research directions. Rapid developments in DNA sequencing technology and bioinformatics will make DNA-based community data increasingly accessible to ecologists, and there needs to be a corresponding shift in research focus from DNA metabarcoding method development and evaluation to real-world applications that provide rich information for a range of purposes, including conservation planning and land management decisions.\r \r **KEYWORDS**\r \r biodiversity monitoring;\r bioinformatics;\r biosecurity;\r cultural indicators;\r ecosystem function;\r environmental DNA;\r national framework;\r species detection;\r te ao maori;\r uncertainty;\r soil food-web;\r environmental DNA;\r microbial communities;\r ancient DNA;\r conservation;\r diversity;\r identification;\r sequences;\r accuracy;\r patterns;""" ; dct:issued "2024-06-26T04:28:34.842147"^^xsd:dateTime ; dct:modified "2024-06-26T04:28:34.842147"^^xsd:dateTime ; dct:title "PAPER: DNA metabarcoding to assess biodiversity" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types###\r \r **February 2018**\r \r **Hermans SM, Buckley HL, Lear G. 2018. [Optimal extraction methods for the simultaneous analysis of DNA from diverse organisms and sample types](https://onlinelibrary.wiley.com/doi/epdf/10.1111/1755-0998.12762). Mol Ecol Resour 18(3): 557-569.**\r \r **ABSTRACT**\r \r Using environmental DNA (eDNA) to assess the distribution of micro- and macroorganisms is becoming increasingly popular. However, the comparability and reliability of these studies is not well understood as we lack evidence on how different DNA extraction methods affect the detection of different organisms, and how this varies among sample types. Our aim was to quantify biases associated with six DNA extraction methods and identify one which is optimal for eDNA research targeting multiple organisms and sample types. We assessed each methods’ ability to simultaneously extract bacterial, fungal, plant, animal and fish DNA from soil, leaf litter, stream water, stream sediment, stream biofilm and kick-net samples, as well as from mock communities. Method choice affected alpha-diversity for several combinations of taxon and sample type, with the majority of the differences occurring in the bacterial communities. While a single method performed optimally for the extraction of DNA from bacterial, fungal and plant mock communities, different methods performed best for invertebrate and fish mock communities. The consistency of methods, as measured by the similarity of community compositions resulting from replicate extractions, varied and was lowest for the animal communities. Collectively, these data provide the first comprehensive assessment of the biases associated with DNA extraction for both different sample types and taxa types, allowing us to identify DNeasy PowerSoil as a universal DNA extraction method. The adoption of standardized approaches for eDNA extraction will ensure that results can be more reliably compared, and biases quantified, thereby advancing eDNA as an ecological research tool.\r \r **KEYWORDS**\r \r DNA extraction; eDNA; environmental DNA; macroorganisms; microorganisms""" ; dct:issued "2024-07-05T03:27:31.388165"^^xsd:dateTime ; dct:modified "2024-07-05T03:27:31.388165"^^xsd:dateTime ; dct:title "PAPER: Extraction methods for simultaneous DNA analysis" ; dcat:accessURL . a dcat:Distribution ; dct:description """###A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations###\r \r **December 2017**\r \r **Laroche O, Wood SA, Tremblay LA, Ellis JI, Lear G, Pochon X 2018. [A cross-taxa study using environmental DNA/RNA metabarcoding to measure biological impacts of offshore oil and gas drilling and production operations.](https://www.sciencedirect.com/science/article/pii/S0025326X17309992/pdfft?md5=0de5d10b61ccfa8ac566552efcc99960&pid=1-s2.0-S0025326X17309992-main.pdf). Mar Pollut Bull 127: 97-107.**\r \r **ABSTRACT**\r \r Standardized ecosystem-based monitoring surveys are critical for providing information on marine ecosystem health. Environmental DNA/RNA (eDNA/eRNA) metabarcoding may facilitate such surveys by quickly and effectively characterizing multi-trophic levels. In this study, we assessed the suitability of eDNA/eRNA metabarcoding to evaluate changes in benthic assemblages of bacteria, Foraminifera and other eukaryotes along transects at three offshore oil and gas (O&G) drilling and production sites, and compared these to morphologically characterized macro-faunal assemblages. Bacterial communities were the most responsive to O&G activities, followed by Foraminifera, and macro-fauna (the latter assessed by morphology). The molecular approach enabled detection of hydrocarbon degrading taxa such as the bacteria Alcanivorax and Microbulbifer at petroleum impacted stations. Most identified indicator taxa, notably among macro-fauna, were highly specific to site conditions. Based on our results we suggest that eDNA/eRNA metabarcoding can be used as a stand-alone method for biodiversity assessment or as a complement to morphology-based monitoring approaches.\r \r **KEYWORDS**\r \r Biomonitoring; Benthic ecology; High-throughput sequencing; Bacteria 16S; Eukaryotes 18S; Foraminifera 18S""" ; dct:issued "2024-07-05T03:46:25.379263"^^xsd:dateTime ; dct:modified "2024-07-05T03:46:25.379263"^^xsd:dateTime ; dct:title "PAPER: A cross-taxa study using environmental DNA/RNA metabarcoding" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Perspectives on the Impact of Sampling Design and Intensity on Soil Microbial Diversity Estimates###\r \r **August 2019**\r \r **Hermans SM, Buckley HL, Lear G. 2019. [Perspectives on the Impact of Sampling Design and Intensity on Soil Microbial Diversity Estimates.](https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.01820/pdf?isPublishedV2=false) Front Microbiol 10(1820): 1820.**\r \r **ABSTRACT** \r \r Soil bacterial communities have long been recognized as important ecosystem components, and have been the focus of many local and regional studies. However, there is a lack of data at large spatial scales, on the biodiversity of soil microorganisms; national or more extensive studies to date have typically consisted of low replication of haphazardly collected samples. This has led to large spatial gaps in soil microbial biodiversity data. Using a pre-existing dataset of bacterial community composition across a 16-km regular sampling grid in France, we show that the number of detected OTUs changes little under different sampling designs (grid, random, or representative), but increases with the number of samples collected. All common OTUs present in the full dataset were detected when analyzing just 4% of the samples, yet the number of rare OTUs increased exponentially with sampling effort. We show that far more intensive sampling, across all global biomes, is required to detect the biodiversity of soil microorganisms. We propose avenues such as citizen science to ensure these large sample datasets can be more realistically achieved. Furthermore, we argue that taking advantage of pre-existing resources and programs, utilizing current technologies efficiently and considering the potential of future technologies will ensure better outcomes from large and extensive sample surveys. Overall, decreasing the spatial gaps in global soil microbial diversity data will increase our understanding on what governs the distribution of soil taxa, and how these distributions, and therefore their ecosystem contributions, will continue to change into the future.\r \r **KEYWORDS**\r \r biodiversity;\r biogeography;\r global datasets;\r national datasets;\r soil bacteria;\r """ ; dct:issued "2024-06-26T03:14:37.596727"^^xsd:dateTime ; dct:modified "2024-06-26T03:14:37.596727"^^xsd:dateTime ; dct:title "PAPER: Impact of Sampling Design and Intensity" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities###\r \r **May 2017**\r \r **Laroche O, Wood SA, Tremblay LA, Lear G, Ellis JI, Pochon X 2017. [Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities.](https://peerj.com/articles/3347.pdf) PeerJ 5: e3347.**\r \r **ABSTRACT**\r \r Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.\r \r **KEYWORDS**\r \r Bacteria (16S);\r Benthic ecology;\r Biomonitoring;\r Eukaryotes (18S);\r High-throughput sequencing;\r Method testing;\r Oil and gas activities;\r eDNA;\r eRNA\r \r """ ; dct:issued "2024-06-26T04:19:39.022314"^^xsd:dateTime ; dct:modified "2024-06-26T04:19:39.022314"^^xsd:dateTime ; dct:title "PAPER: Metabarcoding monitoring analysis" ; dcat:accessURL . a dcat:Distribution ; dct:description """###Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity###\r \r **July 2018**\r \r **Bulman SR, McDougal RL, Hill K, Lear G 2018. [Opportunities and limitations for DNA metabarcoding in Australasian plant-pathogen biosecurity](https://link.springer.com/content/pdf/10.1007/s13313-018-0579-3.pdf). Australasian Plant Pathology 47(5): 467-474.**\r \r **ABSTRACT**\r \r Protecting plants from new pathogen incursions requires effective surveillance practices. Environmental DNA (eDNA) metabarcoding shows considerable promise for detecting invasive organisms in terrestrial and aquatic ecosystems. Metabarcoding is widely used to characterise plant microbiotas and is beginning to be applied to plant biosecurity. However, diagnostic assays for biosecurity must fit within internationally agreed frameworks. Development of new gene targets to improve taxonomic resolution, improved reference databases and simplified bioinformatics platforms are required before phytopathogenic bacteria and fungi can be routinely detected by metabarcoding. Building biodiversity maps from accumulated metabarcoding data represents an important opportunity to define organism presence/absence in New Zealand and Australia and thus to enhance biosecurity decision making. Advances in sequencing technologies and infrastructure promise the creation of eDNA biosecurity surveillance networks from substrates including soil, trapped spores and insects.\r \r **KEYWORDS**\r \r eDNA;\r Sequence databases;\r Detection;\r Surveillance;\r Incursion;\r Microbiota\r \r """ ; dct:issued "2024-07-05T04:27:40.431137"^^xsd:dateTime ; dct:modified "2024-07-05T04:27:40.431137"^^xsd:dateTime ; dct:title "PAPER: Opportunities and limitations for DNA metabarcoding" ; dcat:accessURL . a foaf:Organization ; foaf:name "Challenge Inventory" .