Reforestation is a critical means of addressing the environmental and social problems of deforestation. China's Grain-for-Green Program (GFGP) is the world's largest reforestation scheme. Here we ...provide the first nationwide assessment of the tree composition of GFGP forests and the first combined ecological and economic study aimed at understanding GFGP's biodiversity implications. Across China, GFGP forests are overwhelmingly monocultures or compositionally simple mixed forests. Focusing on birds and bees in Sichuan Province, we find that GFGP reforestation results in modest gains (via mixed forest) and losses (via monocultures) of bird diversity, along with major losses of bee diversity. Moreover, all current modes of GFGP reforestation fall short of restoring biodiversity to levels approximating native forests. However, even within existing modes of reforestation, GFGP can achieve greater biodiversity gains by promoting mixed forests over monocultures; doing so is unlikely to entail major opportunity costs or pose unforeseen economic risks to households.
The accurate extraction of species‐abundance information from DNA‐based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food‐web reconstruction, the inference of ...species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA‐based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within‐sample across‐species quantification describes relative species abundances in one sample. (ii) Across‐sample within‐species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across‐species abundance information (by removing what we call “species pipeline biases”) and within‐species abundance information (by removing what we call “pipeline noise”). We argue that many ecological questions can be answered with just within‐species quantification, and we therefore demonstrate how to use a “DNA spike‐in” to correct for pipeline noise and recover within‐species abundance information. We also introduce a model‐based estimator that can be used on data sets without a physical spike‐in to approximate and correct for pipeline noise.
The very large memory requirements for the construction of assembly graphs for de novo genome assembly limit current algorithms to super-computing environments.
In this paper, we demonstrate that ...constructing a sparse assembly graph which stores only a small fraction of the observed k-mers as nodes and the links between these nodes allows the de novo assembly of even moderately-sized genomes (~500 M) on a typical laptop computer.
We implement this sparse graph concept in a proof-of-principle software package, SparseAssembler, utilizing a new sparse k-mer graph structure evolved from the de Bruijn graph. We test our SparseAssembler with both simulated and real data, achieving ~90% memory savings and retaining high assembly accuracy, without sacrificing speed in comparison to existing de novo assemblers.
Metabarcoding of complex metazoan communities is increasingly being used to measure biodiversity in terrestrial, freshwater and marine ecosystems, revolutionizing our ability to observe patterns and ...infer processes regarding the origin and conservation of biodiversity. A fundamentally important question is which genetic marker to amplify, and although the mitochondrial cytochrome oxidase subunit I (COI) gene is one of the more widely used markers in metabarcoding for the Metazoa, doubts have recently been raised about its suitability. We argue that (a) the extensive coverage of reference sequence databases for COI; (b) the variation it presents; (c) the comparative advantages for denoising protein‐coding genes; and (d) recent advances in DNA sequencing protocols argue in favour of standardizing for the use of COI for metazoan community samples. We also highlight where research efforts should focus to maximize the utility of metabarcoding.
•eDNA is driving rapid advances in ecology, evolution, and conservation.•eDNA provides mechanistic insights into ecological and evolutionary processes.•Foremost among these is an improved ability to ...explore ecosystem-level processes.•We examine current frontiers of eDNA, outlining key aspects requiring improvement.•We suggest future developments and priorities for eDNA research.
Extraction and identification of DNA from an environmental sample has proven noteworthy recently in detecting and monitoring not only common species, but also those that are endangered, invasive, or elusive. Particular attributes of so-called environmental DNA (eDNA) analysis render it a potent tool for elucidating mechanistic insights in ecological and evolutionary processes. Foremost among these is an improved ability to explore ecosystem-level processes, the generation of quantitative indices for analyses of species, community diversity, and dynamics, and novel opportunities through the use of time-serial samples and unprecedented sensitivity for detecting rare or difficult-to-sample taxa. Although technical challenges remain, here we examine the current frontiers of eDNA, outline key aspects requiring improvement, and suggest future developments and innovations for research.
Attine ants are dependent on a cultivated fungus for food and use antibiotics produced by symbiotic Actinobacteria as weedkillers in their fungus gardens. Actinobacterial species belonging to the ...genera Pseudonocardia, Streptomyces and Amycolatopsis have been isolated from attine ant nests and shown to confer protection against a range of microfungal weeds. In previous work on the higher attine Acromyrmex octospinosus we isolated a Streptomyces strain that produces candicidin, consistent with another report that attine ants use Streptomyces-produced candicidin in their fungiculture. Here we report the genome analysis of this Streptomyces strain and identify multiple antibiotic biosynthetic pathways. We demonstrate, using gene disruptions and mass spectrometry, that this single strain has the capacity to make candicidin and multiple antimycin compounds. Although antimycins have been known for >60 years we report the sequence of the biosynthetic gene cluster for the first time. Crucially, disrupting the candicidin and antimycin gene clusters in the same strain had no effect on bioactivity against a co-evolved nest pathogen called Escovopsis that has been identified in ∼30% of attine ant nests. Since the Streptomyces strain has strong bioactivity against Escovopsis we conclude that it must make additional antifungal(s) to inhibit Escovopsis. However, candicidin and antimycins likely offer protection against other microfungal weeds that infect the attine fungal gardens. Thus, we propose that the selection of this biosynthetically prolific strain from the natural environment provides A. octospinosus with broad spectrum activity against Escovopsis and other microfungal weeds.
The Honghe-Hani landscape in China is a UNESCO World Natural Heritage site due to the beauty of its thousands of rice terraces, but these structures are in danger from the invasive crayfish ...Procambarus clarkii. Crayfish dig nest holes, which collapse terrace walls and destroy rice production. Under the current control strategy, farmers self-report crayfish and are issued pesticide, but this strategy is not expected to eradicate the crayfish nor to prevent their spread since farmers are not able to detect small numbers of crayfish. Thus, we tested whether environmental DNA (eDNA) from paddy-water samples could provide a sensitive detection method. In an aquarium experiment, Real-time Quantitative polymerase chain reaction (qPCR) successfully detected crayfish, even at a simulated density of one crayfish per average-sized paddy (with one false negative). In a field test, we tested eDNA and bottle traps against direct counts of crayfish. eDNA successfully detected crayfish in all 25 paddies where crayfish were observed and in none of the 7 paddies where crayfish were absent. Bottle-trapping was successful in only 68% of the crayfish-present paddies. eDNA concentrations also correlated positively with crayfish counts. In sum, these results suggest that single samples of eDNA are able to detect small crayfish populations, but not perfectly. Thus, we conclude that a program of repeated eDNA sampling is now feasible and likely reliable for measuring crayfish geographic range and for detecting new invasion fronts in the Honghe Hani landscape, which would inform regional control efforts and help to prevent the further spread of this invasive crayfish.
Summary
1. Traditional biodiversity assessment is costly in time, money and taxonomic expertise. Moreover, data are frequently collected in ways (e.g. visual bird lists) that are unsuitable for ...auditing by neutral parties, which is necessary for dispute resolution.
2. We present protocols for the extraction of ecological, taxonomic and phylogenetic information from bulk samples of arthropods. The protocols combine mass trapping of arthropods, mass‐PCR amplification of the COI barcode gene, pyrosequencing and bioinformatic analysis, which together we call ‘metabarcoding’.
3. We construct seven communities of arthropods (mostly insects) and show that it is possible to recover a substantial proportion of the original taxonomic information. We further demonstrate, for the first time, that metabarcoding allows for the precise estimation of pairwise community dissimilarity (beta diversity) and within‐community phylogenetic diversity (alpha diversity), despite the inevitable loss of taxonomic information inherent to metabarcoding.
4. Alpha and beta diversity metrics are the raw materials of ecology and the environmental sciences, facilitating assessment of the state of the environment with a broad and efficient measure of biodiversity.
Presentation
There is great interest in explaining how beneficial microbiomes are assembled. Antibiotic‐producing microbiomes are arguably the most abundant class of beneficial microbiome in nature, having been ...found on corals, arthropods, molluscs, vertebrates and plant rhizospheres. An exemplar is the attine ants, which cultivate a fungus for food and host a cuticular microbiome that releases antibiotics to defend the fungus from parasites. One explanation posits long‐term vertical transmission of Pseudonocardia bacteria, which (somehow) evolve new compounds in arms‐race fashion against parasites. Alternatively, attines (somehow) selectively recruit multiple, non‐coevolved actinobacterial genera from the soil, enabling a ‘multi‐drug’ strategy against parasites. We reconcile the models by showing that when hosts fuel interference competition by providing abundant resources, the interference competition favours the recruitment of antibiotic‐producing (and ‐resistant) bacteria. This partner‐choice mechanism is more effective when at least one actinobacterial symbiont is vertically transmitted or has a high immigration rate, as in disease‐suppressive soils.
To manage and conserve biodiversity, one must know what is being lost, where, and why, as well as which remedies are likely to be most effective. Metabarcoding technology can characterise the species ...compositions of mass samples of eukaryotes or of environmental DNA. Here, we validate metabarcoding by testing it against three high‐quality standard data sets that were collected in Malaysia (tropical), China (subtropical) and the United Kingdom (temperate) and that comprised 55,813 arthropod and bird specimens identified to species level with the expenditure of 2,505 person‐hours of taxonomic expertise. The metabarcode and standard data sets exhibit statistically correlated alpha‐ and beta‐diversities, and the two data sets produce similar policy conclusions for two conservation applications: restoration ecology and systematic conservation planning. Compared with standard biodiversity data sets, metabarcoded samples are taxonomically more comprehensive, many times quicker to produce, less reliant on taxonomic expertise and auditable by third parties, which is essential for dispute resolution.
PDF
