Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt (Triturus cristatus)

Environmental DNA (eDNA) analysis is a rapid, cost-effective, non-invasive biodiversity monitoring tool which utilises DNA left behind in the environment by organisms for species detection. The method is used as a species-specific survey tool for rare or invasive species across a broad range of ecosystems. Recently, eDNA and "metabarcoding" have been combined to describe whole communities rather than focusing on single target species. However, whether metabarcoding is as sensitive as targeted approaches for rare species detection remains to be evaluated. The great crested newt Triturus cristatus is a flagship pond species of international conservation concern and the first UK species to be routinely monitored using eDNA. We evaluate whether eDNA metabarcoding has comparable sensitivity to targeted real-time quantitative PCR (qPCR) for T. cristatus detection. Extracted eDNA samples (N = 532) were screened for T. cristatus by qPCR and analysed for all vertebrate species using high-throughput sequencing technology. With qPCR and a detection threshold of 1 of 12 positive qPCR replicates, newts were detected in 50% of ponds. Detection decreased to 32% when the threshold was increased to 4 of 12 positive qPCR replicates. With metabarcoding, newts were detected in 34% of ponds without a detection threshold, and in 28% of ponds when a threshold (0.028%) was applied. Therefore, qPCR provided greater detection than metabarcoding but metabarcoding detection with no threshold was equivalent to qPCR with a stringent detection threshold. The proportion of T. cristatus sequences in each sample was positively associated with the number of positive qPCR replicates (qPCR score) suggesting eDNA metabarcoding may be indicative of eDNA concentration. eDNA metabarcoding holds enormous potential for holistic biodiversity assessment and routine freshwater monitoring. We advocate this community approach to freshwater monitoring to guide management and conservation, whereby entire communities can be initially surveyed to best inform use of funding and time for species-specific surveys.

Population-level inferences from environmental DNA-Current status and future perspectives

Environmental DNA (eDNA) extracted from water samples has recently shown potential as a valuable source of population genetic information for aquatic macroorganisms. This approach offers several potential advantages compared with conventional tissue-based methods, including the fact that eDNA sampling is noninvasive and generally more cost-efficient. Currently, eDNA approaches have been limited to single-marker studies of mitochondrial DNA (mtDNA), and the relationship between eDNA haplotype composition and true haplotype composition still needs to be thoroughly verified. This will require testing of bioinformatic and statistical software to correct for erroneous sequences, as well as biases and random variation in relative sequence abundances. However, eDNA-based population genetic methods have far-reaching potential for both basic and applied research. In this paper, we present a brief overview of the achievements of eDNA-based population genetics to date, and outline the prospects for future developments in the field, including the estimation of nuclear DNA (nuDNA) variation and epigenetic information. We discuss the challenges associated with eDNA samples as opposed to those of individual tissue samples and assess whether eDNA might offer additional types of information unobtainable with tissue samples. Lastly, we provide recommendations for determining whether an eDNA approach would be a useful and suitable choice in different research settings. We limit our discussion largely to contemporary aquatic systems, but the advantages, challenges, and perspectives can to a large degree be generalized to eDNA studies with a different spatial and temporal focus.

Deciphering factors driving soil microbial life-history strategies in restored grasslands

In macroecology, the concept of r- and K-strategy has been widely applied, yet, there have been limited studies on microbial life-history strategies in temperate grasslands using multiple sequencing approaches. Total phospholipid fatty acid (PLFA) analysis, high-throughput meta-genomic sequencing, and GeoChip technologies were used to examine the changes in microbial life-history traits in a chronosequence of restored grasslands (1, 5, 10, 15, 25, and 30 years since restoration). Grassland restoration increased the relative abundances of Actinobacteria, Proteobacteria, and Bacteroidetes but reduced the relative abundances of Acidobacteria, Planctomycetes, and Chloroflexi. PLFA analysis revealed that grassland restoration reduced the fungi:bacteria and Gram-positive:Gram-negative bacteria ratios. Combined with the meta-genomic data, we found that grassland restoration shifted microorganisms from oligotrophic (K-) to copiotrophic (r-) groups, consistent with the increased rRNA operon copy number of the microbial community. Structural equation modeling showed that soil properties positively (p < 0.05) while plant properties negatively (p < 0.05) affected microbial life-history traits. We built a framework to highlight the importance of plant and soil properties in driving microbial life-history traits during grassland restoration. Finally, by incorporating meta-genomic and other microbiological data, this study showed that microbial life-history traits support the idea that rRNA operon copy number is a trait that reflects resource availability to soil microorganisms.

Toward an ecoregion scale evaluation of eDNA metabarcoding primers: A case study for the freshwater fish biodiversity of the Murray-Darling Basin (Australia)

High-throughput sequencing of environmental DNA (i.e., eDNA metabarcoding) has become an increasingly popular method for monitoring aquatic biodiversity. At present, such analyses require target-specific primers to amplify DNA barcodes from co-occurring species, and this initial amplification can introduce biases. Understanding the performance of different primers is thus recommended prior to undertaking any metabarcoding initiative. While multiple software programs are available to evaluate metabarcoding primers, all programs have their own strengths and weaknesses. Therefore, a robust in silico workflow for the evaluation of metabarcoding primers will benefit from the use of multiple programs. Furthermore, geographic differences in species biodiversity are likely to influence the performance of metabarcoding primers and further complicate the evaluation process. Here, an in silico workflow is presented that can be used to evaluate the performance of metabarcoding primers on an ecoregion scale. This workflow was used to evaluate the performance of published and newly developed eDNA metabarcoding primers for the freshwater fish biodiversity of the Murray-Darling Basin (Australia). To validate the in silico workflow, a subset of the primers, including one newly designed primer pair, were used in metabarcoding analyses of an artificial DNA community and eDNA samples. The results show that the in silico workflow allows for a robust evaluation of metabarcoding primers and can reveal important trade-offs that need to be considered when selecting the most suitable primer. Additionally, a new primer pair was described and validated that allows for more robust taxonomic assignments and is less influenced by primer biases compared to commonly used fish metabarcoding primers.

Engineered Tools to Study Intercellular Communication

All multicellular organisms rely on intercellular communication networks to coordinate physiological functions. As members of a dynamic social network, each cell receives, processes, and redistributes biological information to define and maintain tissue homeostasis. Uncovering the molecular programs underlying these processes is critical for prevention of disease and aging and development of therapeutics. The study of intercellular communication requires techniques that reduce the scale and complexity of in vivo biological networks while resolving the molecular heterogeneity in "omic" layers that contribute to cell state and function. Recent advances in microengineering and high-throughput genomics offer unprecedented spatiotemporal control over cellular interactions and the ability to study intercellular communication in a high-throughput and mechanistic manner. Herein, this review discusses how salient engineered approaches and sequencing techniques can be applied to understand collective cell behavior and tissue functions.

The impact of OTU sequence similarity threshold on diatom-based bioassessment: A case study of the rivers of Mayotte (France, Indian Ocean)

Extensive studies on the taxonomic resolution required for bioassessment purposes have determined that resolution above species level (genus, family) is sufficient for their use as indicators of relevant environmental pressures. The high-throughput sequencing (HTS) and meta-barcoding methods now used for bioassessment traditionally employ an arbitrary sequence similarity threshold (SST) around 95% or 97% to cluster sequences into operational taxonomic units, which is considered descriptive of species-level resolution. In this study, we analyzed the effect of the SST on the resulting diatom-based ecological quality index, which is based on OTU abundance distribution along a defined environmental gradient, ideally avoiding taxonomic assignments that could result in high rates of unclassified OTUs and biased final values. A total of 90 biofilm samples were collected in 2014 and 2015 from 51 stream sites on Mayotte Island in parallel with measures of relevant physical and chemical parameters. HTS sequencing was performed on the biofilms using the rbcL region as the genetic marker and diatom-specific primers. Hierarchical clustering was used to group sequences into OTUs using 20 experimental SST levels (80%-99%). An OTU-based quality index (IdxOTU) was developed based on a weighted average equation using the abundance profiles of the OTUs. The developed IdxOTU revealed significant correlations between the IdxOTU values and the reference pressure gradient, which reached maximal performance using an SST of 90% (well above species level delimitation). We observed an interesting and important trade-off with the power to discriminate between sampling sites and index stability that will greatly inform future applications of the index. Taken together, the results from this study detail a thoroughly optimized and validated approach to generating robust, reproducible, and complete indexes that will greatly facilitate effective and efficient environmental monitoring.

Insights into the bacterial symbiont diversity in spiders

Most spiders are natural enemies of pests, and it is beneficial for the biological control of pests to learn the relationships between symbionts and their spider hosts. Research on the bacterial communities of insects has been conducted recently, but only a few studies have addressed the bacterial communities of spiders. To obtain a complete overview of the microbial communities of spiders, we examined eight species of spider (Pirata subpiraticus, Agelena difficilis, Artema atlanta, Nurscia albofasciata, Agelena labyrinthica, Ummeliata insecticeps, Dictis striatipes, and Hylyphantes graminicola) with high-throughput sequencing based on the V3 and V4 regions of the 16S rRNA gene. The bacterial communities of the spider samples were dominated by five types of endosymbionts, Wolbachia, Cardinium, Rickettsia, Spiroplasma, and Rickettsiella. The dominant OTUs (operational taxonomic units) from each of the five endosymbionts were analyzed, and the results showed that different spider species were usually dominated by special OTUs. In addition to endosymbionts, Pseudomonas, Sphingomonas, Acinetobacter, Novosphingobium, Aquabacterium, Methylobacterium, Brevundimonas, Rhizobium, Bradyrhizobium, Citrobacter, Arthrobacter, Pseudonocardia, Microbacterium, Lactobacillus, and Lactococcus were detected in spider samples in our study. Moreover, the abundance of Sphingomonas, Methylobacterium, Brevundimonas, and Rhizobium in the spider D. striatipes was significantly higher (p < .05) than the bacterial abundance of these species in seven other spider species. These findings suggest that same as in insects, co-infection of multiple types of endosymbionts is common in the hosts of the Araneae order, and other bacterial taxa also exist in spiders besides the endosymbionts.

Invasion genetics from eDNA and thousands of larvae: A targeted metabarcoding assay that distinguishes species and population variation of zebra and quagga mussels

Identifying species and population genetic compositions of biological invasions at early life stages and/or from environmental (e)DNA using targeted high-throughput sequencing (HTS) metabarcode assays offers powerful and cost-effective means for early detection, analysis of spread patterns, and evaluating population changes. The present study develops, tests, and applies this method with a targeted sequence assay designed to simultaneously identify and distinguish between the closely related invasive Eurasian zebra and quagga mussels (Dreissena polymorpha and D. rostriformis) and their relatives and discern their respective population genetic patterns. Invasions of these dreissenid mussel species have markedly changed freshwater ecosystems throughout North America and Europe, exerting severe ecological and economic damage. Their planktonic early life stages (eggs and larvae) are morphologically indistinguishable, yet each species exerts differential ecological effects, with the quagga often outcompeting the zebra mussel as adults. Our targeted assay analyzes genetic variation from a diagnostic sequence region of the mitochondrial (mt)DNA cytochrome oxidase I (COI) gene, to assess temporal and spatial inter- and intra-specific genetic variability. The assay facilitates analysis of environmental (e)DNA from water, early life stages from thousands of individuals, and simultaneous analysis of 50-100 tagged field-collected samples. Experiments evaluated its accuracy and performance using: (a) mock laboratory communities containing known DNA quantities per taxon, (b) aquaria with mixed-species/haplotype compositions of adults, and (c) field-collected water and plankton versus traditional sampling of adult communities. Results delineated species compositions, relative abundances, and population-level diversity differences among ecosystems, habitats, time series, and life stages from two allopatric concurrent invasions in the Great Lakes (Lake Erie) and the Hudson River, which had separate founding histories. Findings demonstrate application of this targeted assay and our approach to accurately and simultaneously discern species- and population-level differences across spatial and temporal scales, facilitating early detection and ecological understanding of biological invasions.

Soil physicochemical properties drive the variation in soil microbial communities along a forest successional series in a degraded wetland in northeastern China

The Sanjiang Plain is the biggest freshwater wetland locating in northeastern China. Due to climate change and human activities, that wetland has degraded to a successional gradient from the original flooded wetland to dry shrub vegetation and a forest area with lower ground water level, which may result in changes in soil microbiologic structure and functions. The present study investigated the microbial diversity and community structure in relation to soil properties along that successional gradient. The soil physico-chemical properties changed significantly with degradation stage. The Shannon diversity index of both soil bacteria (5.90-6.42) and fungi (1.7-4.19) varied significantly with successional stage (both p < .05). The community structures of soil bacteria and fungi in the early successional stages (i.e., the wetland) were significantly determined by water content, total nitrogen, and available nitrogen concentrations in soils, while those in the later successional stages (i.e., forests) were significantly structured by soil organic carbon, soil pH, and available phosphorus concentrations. These results suggest that the soil microbial structure is mainly determined by soil properties rather than by plant community such as plant species composition along successional stages.

Optimization and performance testing of a sequence processing pipeline applied to detection of nonindigenous species

Genetic taxonomic assignment can be more sensitive than morphological taxonomic assignment, particularly for small, cryptic or rare species. Sequence processing is essential to taxonomic assignment, but can also produce errors because optimal parameters are not known a priori. Here, we explored how sequence processing parameters influence taxonomic assignment of 18S sequences from bulk zooplankton samples produced by 454 pyrosequencing. We optimized a sequence processing pipeline for two common research goals, estimation of species richness and early detection of aquatic invasive species (AIS), and then tested most optimal models' performances through simulations. We tested 1,050 parameter sets on 18S sequences from 20 AIS to determine optimal parameters for each research goal. We tested optimized pipelines' performances (detectability and sensitivity) by computationally inoculating sequences of 20 AIS into ten bulk zooplankton samples from ports across Canada. We found that optimal parameter selection generally depends on the research goal. However, regardless of research goal, we found that metazoan 18S sequences produced by 454 pyrosequencing should be trimmed to 375-400 bp and sequence quality filtering should be relaxed (1.5 ≤ maximum expected error ≤ 3.0, Phred score = 10). Clustering and denoising were only viable for estimating species richness, because these processing steps made some species undetectable at low sequence abundances which would not be useful for early detection of AIS. With parameter sets optimized for early detection of AIS, 90% of AIS were detected with fewer than 11 target sequences, regardless of whether clustering or denoising was used. Despite developments in next-generation sequencing, sequence processing remains an important issue owing to difficulties in balancing false-positive and false-negative errors in metabarcoding data.

Secondary contacts and genetic admixture shape colonization by an amphiatlantic epibenthic invertebrate

Research on the genetics of invasive species often focuses on patterns of genetic diversity and population structure within the introduced range. However, a growing body of literature is demonstrating the need to study how native genotypes affect both ecological and evolutionary mechanisms within the introduced range. Here, we used genotyping-by-sequencing to study both native and introduced ranges of the amphiatlantic marine invertebrate Ciona intestinalis. A previous study using microsatellites analysed samples collected along the Swedish west coast and showed the presence of genetically distinct lineages in deep and shallow waters. Using 1,653 single nucleotide polymorphisms (SNPs) from newly collected samples (285 individuals), we first confirmed the presence of this depth-defined genomic divergence along the Swedish coast. We then used approximate Bayesian computation to infer the historical relationship among sites from the North Sea, the English Channel and the northwest Atlantic and found evidence of ancestral divergence between individuals from deep waters off Sweden and individuals from the English Channel. This divergence was followed by a secondary contact that led to a genetic admixture between the ancestral populations (i.e., deep Sweden and English Channel), which originated the genotypes found in shallow Sweden. We then revealed that the colonization of C. intestinalis in the northwest Atlantic was as a result of an admixture between shallow Sweden and the English Channel genotypes across the introduced range. Our results showed the presence of both past and recent genetic admixture events that together may have promoted the successful colonizations of C. intestinalis. Our study suggests that secondary contacts potentially reshape the evolutionary trajectories of invasive species through the promotion of intraspecific hybridization and by altering both colonization patterns and their ecological effects in the introduced range.

Unlocking the potential of ancient fish DNA in the genomic era

Fish are the most diverse group of vertebrates, fulfil important ecological functions and are of significant economic interest for aquaculture and wild fisheries. Advances in DNA extraction methods, sequencing technologies and bioinformatic applications have advanced genomic research for nonmodel organisms, allowing the field of fish ancient DNA (aDNA) to move into the genomics era. This move is enabling researchers to investigate a multitude of new questions in evolutionary ecology that could not, until now, be addressed. In many cases, these new fields of research have relevance to evolutionary applications, such as the sustainable management of fisheries resources and the conservation of aquatic animals. Here, we focus on the application of fish aDNA to (a) highlight new research questions, (b) outline methodological advances and current challenges, (c) discuss how our understanding of fish ecology and evolution can benefit from aDNA applications and (d) provide a future perspective on how the field will help answer key questions in conservation and management. We conclude that the power of fish aDNA will be unlocked through the application of continually improving genomic resources and methods to well-chosen taxonomic groups represented by well-dated archaeological samples that can provide temporally and/or spatially extensive data sets.

Dominant plant species shape soil bacterial community in semiarid sandy land of northern China

Plant species affect soil bacterial diversity and compositions. However, little is known about the role of dominant plant species in shaping the soil bacterial community during the restoration of sandy grasslands in Horqin Sandy Land, northern China. We established a mesocosm pots experiment to investigate short-term responses of soil bacterial diversity and composition, and the related soil properties in degraded soils without vegetation (bare sand as the control, CK) to restoration with five plant species that dominate across restoration stages: Agriophyllum squarrosum (AS), Artemisia halodendron (AH), Setaria viridis (SV), Chenopodium acuminatum (CA), and Corispermum macrocarpum (CM). We used redundancy analysis (RDA) to analyze the association between soil bacterial composition and soil properties in different plant species. Our results indicated that soil bacterial diversity was significantly lower in vegetated soils independent of plant species than in the CK. Specifically, soil bacterial species richness and diversity were lower under the shrub AH and the herbaceous plants AS, SV, and CA, and soil bacterial abundance was lower under AH compared with the CK. A field investigation confirmed the same trends where soil bacteria diversity was lower under AS and AH than in bare sand. The high-sequence annotation analysis showed that Proteobacteria, Actinobacteria, and Bacteroidetes were the most common phyla in sandy land irrespective of soil plant cover. The OTUs (operational taxonomic units) indicated that some bacterial species were specific to the host plants. Relative to bare sand (CK), soils with vegetative cover exhibited lower soil water content and temperature, and higher soil carbon and nitrogen contents. The RDA result indicated that, in addition to plant species, soil water and nitrogen contents were the most important factors shaping soil bacterial composition in semiarid sandy land. Our study from the pot and field investigations clearly demonstrated that planting dominant species in bare sand impacts bacterial diversity. In semiarid ecosystems, changes in the dominant plant species during vegetation restoration efforts can affect the soil bacterial diversity and composition through the direct effects of plants and the indirect effects of soil properties that are driven by plant species.

What is the "modified" CTAB protocol? Characterizing modifications to the CTAB DNA extraction protocol

Cetyltrimethylammonium bromide (CTAB)-based methods are widely used to isolate DNA from plant tissues, but the unique chemical composition of secondary metabolites among plant species has necessitated optimization. Research articles often cite a "modified" CTAB protocol without explicitly stating how the protocol had been altered, creating non-reproducible studies. Furthermore, the various modifications that have been applied to the CTAB protocol have not been rigorously reviewed and doing so could reveal optimization strategies across study systems. We surveyed the literature for modified CTAB protocols used for the isolation of plant DNA. We found that every stage of the CTAB protocol has been modified, and we summarized those modifications to provide recommendations for extraction optimization. Future genomic studies will rely on optimized CTAB protocols. Our review of the modifications that have been used, as well as the protocols we provide here, could better standardize DNA extractions, allowing for repeatable and transparent studies.

Advancing biodiversity assessments with environmental DNA: Long-read technologies help reveal the drivers of Amazonian fungal diversity

Fungi are a key component of tropical biodiversity. However, due to their inconspicuous and largely subterranean nature, they are usually neglected in biodiversity inventories. The goal of this study was to identify the key determinants of fungal richness, community composition, and turnover in tropical rainforests. We tested specifically for the effect of soil properties, habitat, and locality in Amazonia. For these analyses, we used high-throughput sequencing data of short and long reads of fungal DNA present in soil and organic litter samples, combining existing and novel genomic data. Habitat type (phytophysiognomy) emerges as the strongest factor explaining fungal community composition. Naturally open areas-campinas-are the richest habitat overall. Soil properties have different effects depending on the soil layer (litter or mineral soil) and the choice of genetic marker. We suggest that campinas could be a neglected hotspot of fungal diversity. An underlying cause for their rich diversity may be the overall low soil fertility, which increases the reliance on biotic interactions essential for nutrient absorption in these environments, notably ectomycorrhizal fungi-plant associations. Our results highlight the advantages of using both short and long DNA reads produced through high-throughput sequencing to characterize fungal diversity. While short reads can suffice for diversity and community comparison, long reads add taxonomic precision and have the potential to reveal population diversity.

Geographical distribution of zooplankton biodiversity in highly polluted running water ecosystems: Validation of fine-scale species sorting hypothesis

Dispersal, rather than species sorting, is widely recognized as the dominant driver for determining meta-community structure at fine geographical scales in running water ecosystems. However, this view has been challenged by a recently proposed "fine-scale species sorting hypothesis," where community structure can be largely determined by an environmental gradient formed by local pollution at fine scales. Here, we tested this hypothesis by studying community composition and geographical distribution of metazoan zooplankton in a heavily polluted river-the North Canal River in the Haihe River Basin, China. Analysis of similarity (ANOSIM) showed that the community composition of metazoan zooplankton differed significantly (p = .001) along the environmental gradient. Ammonium (NH4-N) was the leading factor responsible for changes in zooplankton community structure and geographical distribution, followed by total dissolved solid (TDS), Na, dissolved oxygen (DO) and temperature (T). Variation partitioning revealed a larger contribution of environmental variables (21.6%) than spatial variables (1.1%) to the total explained variation of zooplankton communities. Our results support that species sorting, rather than dispersal, played a key role in structuring communities. Threshold Indicator Taxa ANalysis (TITAN) also revealed significant change points at both taxon and community levels along the gradient of NH4-N, providing further support for the influence of environmental variables on zooplankton communities. Collectively, we validate the fine-scale species sorting hypothesis when an environmental gradient exists in running water ecosystems at fine geographical scales. However, future studies on interactions between pollutants and zooplankton communities are still needed to better understand mechanisms responsible for the meta-community dynamics.

Compound Fu brick tea modifies the intestinal microbiome composition in high-fat diet-induced obesity mice

Compound Fu Brick Tea (CFBT), which is from Duyun city in China, is a traditional Chinese dark tea, Fu Brick Tea, mixed with six herbal medicine. It is consumed by local people for reducing weight, but the mechanism is not clear. The disorder of intestinal microbiome caused by long-term high-fat diet (HFD) is one of the inducements of obesity and related metabolic syndrome. In this study, mice were fed with HFD to establish a high-fat model. Fifty mice were randomly divided into six groups: normal control (CK), HFD model control (NK), positive control with medicine (YK), CFBT groups with low, middle, and high dose (FL, FM, FH). The V3-V4 DNA region of fecal microbiome from mouse intestine was sequenced. The results showed that the diversity of intestinal microflora was highest in CK and lowest in NK. Compared with CK, the dominant bacterium Firmicutes was increased and Bacteroidetes decreased at phylum level in NK. Compared with NK, the abundance of microbiome in CFBT groups was significantly higher and the composition was changed: Muribaculaceae, Bacteroidaceae, and Prevotellaceae increased and Lachnospiraceae decreased in CFBT groups at family level, while at the genus level, Bacteroides increased and Lactobacillus decreased. These results conclude that CFBT can increase the abundance of intestinal microbiome in mice, promote the growth of beneficial bacteria and reduce the number of pathogenic bacteria, and restore the imbalance of intestinal microbiome caused by poor diet.

Analysis of microbial diversity and succession during Xiaoqu Baijiu fermentation using high-throughput sequencing technology

In this study, high-throughput sequencing (HTS) was used to compare and analyze the microbial diversity and succession during the brewing process of xiaoqu Baijiu. A total of 34 phyla and 378 genera of bacteria, as well as four phyla, 32 genera of fungi were detected. At the phylum level, Firmicutes, Proteobacteria, Ascomycota, and Mucoromycota were the dominant groups. During the brewing process of xiaoqu Baijiu, the dominant bacteria were Weissella and unidentified Rickettsiales within the first 2 days of brewing, followed by Lactobacillus at 3 days until to the end of brewing. The dominant fungi were Rhizopus, Saccharomyces, and Issatchenkia. The relative abundance of Rhizopus decreased with the extension of brewing time, while the relative abundance of Saccharomyces increased, and Saccharomyces became the dominant species at the second day of brewing. This study revealed the diversity and changes of the microbial community during the brewing process of xiaoqu Baijiu, providing theoretical support and laying a foundation for future study on the contribution of microbial metabolism during brewing of xiaoqu Baijiu, thereby promoting the development of xiaoqu Baijiu industry.

PhyloHerb: A high-throughput phylogenomic pipeline for processing genome skimming data

Premise

The application of high-throughput sequencing, especially to herbarium specimens, is rapidly accelerating biodiversity research. Low-coverage sequencing of total genomic DNA (genome skimming) is particularly promising and can simultaneously recover the plastid, mitochondrial, and nuclear ribosomal regions across hundreds of species. Here, we introduce PhyloHerb, a bioinformatic pipeline to efficiently assemble phylogenomic data sets derived from genome skimming.

Methods and Results

PhyloHerb uses either a built-in database or user-specified references to extract orthologous sequences from all three genomes using a BLAST search. It outputs FASTA files and offers a suite of utility functions to assist with alignment, partitioning, concatenation, and phylogeny inference. The program is freely available at https://github.com/lmcai/PhyloHerb/.

Conclusions

We demonstrate that PhyloHerb can accurately identify genes using a published data set from Clusiaceae. We also show via simulations that our approach is effective for highly fragmented assemblies from herbarium specimens and is scalable to thousands of species.

From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next-generation sequencing approaches have prompted the transition to genome-wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double-digest restriction-associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild-born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.

Integrative analysis of genome-wide lncRNA and mRNA expression in newly synthesized Brassica hexaploids

Polyploidization, as a significant evolution force, has been considered to facilitate plant diversity. The expression levels of lncRNAs and how they control the expression of protein-coding genes in allopolyploids remain largely unknown. In this study, lncRNA expression profiles were compared between Brassica hexaploid and its parents using a high-throughput sequencing approach. A total of 2,725, 1,672, and 2,810 lncRNAs were discovered in Brassica rapa, Brassica carinata, and Brassica hexaploid, respectively. It was also discovered that 725 lncRNAs were differentially expressed between Brassica hexaploid and its parents, and 379 lncRNAs were nonadditively expressed in this hexaploid. LncRNAs have multiple expression patterns between Brassica hexaploid and its parents and show paternal parent-biased expression. These lncRNAs were found to implement regulatory functions directly in the long-chain form, and acted as precursors or targets of miRNAs. According to the prediction of the targets of differentially expressed lncRNAs, 109 lncRNAs were annotated, and their target genes were involved in the metabolic process, pigmentation, reproduction, exposure to stimulus, biological regulation, and so on. Compared with the paternal parent, differentially expressed lncRNAs between Brassica hexaploid and its maternal parent participated in more regulation pathways. Additionally, 61 lncRNAs were identified as putative targets of known miRNAs, and 15 other lncRNAs worked as precursors of miRNAs. Some conservative motifs of lncRNAs from different groups were detected, which indicated that these motifs could be responsible for their regulatory roles. Our findings may provide a reference for the further study of the function and action mechanisms of lncRNAs during plant evolution.

In silico and empirical evaluation of twelve metabarcoding primer sets for insectivorous diet analyses

During the most recent decade, environmental DNA metabarcoding approaches have been both developed and improved to minimize the biological and technical biases in these protocols. However, challenges remain, notably those relating to primer design. In the current study, we comprehensively assessed the performance of ten COI and two 16S primer pairs for eDNA metabarcoding, including novel and previously published primers. We used a combined approach of in silico, in vivo-mock community (33 arthropod taxa from 16 orders), and guano-based analyses to identify primer sets that would maximize arthropod detection and taxonomic identification, successfully identify the predator (bat) species, and minimize the time and financial costs of the experiment. We focused on two insectivorous bat species that live together in mixed colonies: the greater horseshoe bat (Rhinolophus ferrumequinum) and Geoffroy's bat (Myotis emarginatus). We found that primer degeneracy is the main factor that influences arthropod detection in silico and mock community analyses, while amplicon length is critical for the detection of arthropods from degraded DNA samples. Our guano-based results highlight the importance of detecting and identifying both predator and prey, as guano samples can be contaminated by other insectivorous species. Moreover, we demonstrate that amplifying bat DNA does not reduce the primers' capacity to detect arthropods. We therefore recommend the simultaneous identification of predator and prey. Finally, our results suggest that up to one-third of prey occurrences may be unreliable and are probably not of primary interest in diet studies, which may decrease the relevance of combining several primer sets instead of using a single efficient one. In conclusion, this study provides a pragmatic framework for eDNA primer selection with respect to scientific and methodological constraints.

A broadly applicable COI primer pair and an efficient single-tube amplicon library preparation protocol for metabarcoding

The nucleotide variation in the cytochrome c oxidase subunit I (COI) gene makes it ideal for assigning sequences to species. However, this variability also makes it difficult to design truly universal primers. Here, we present the forward primer "Sauron-S878," specifically designed to facilitate library preparation for metabarcoding. This primer is modified to improve the coverage of terrestrial species compared to the primer mCOIintF, optimized for aquatic systems, which raised the in silico coverage from 74.4% to 98.3% of available NCBI sequences (perfect match in 3' region, up to three mismatches in remaining primer). When paired with the reverse primer "jgHCO2198" (fragment length ~313 bp), these primers amplified 98.4% of 255 tested DNA extracts from various taxa, which are better than many other common COI barcoding primers. Furthermore, a single-tube protocol was developed, wherein these primers amplify the target gene, and attach MIDs and Illumina sequencing adapters in one reaction. This eliminates the need for re-amplification or enzymatic ligation during library preparation while keeping the flexibility to modularly combine primers and MIDs. Using the single-tube approach, three replicates of three mock samples were sequenced on a MiSeq platform with no adverse effects compared to commercial Nextera indexing kits. From this run, 75% of all included taxa could be recovered, with no considerable bias among taxonomic groups. Despite the fact that 98.4% of the extracts were confirmed to amplify in vitro, this number was lower than expected. A reason for this discrepancy was a clear link between the relative concentration of a specific DNA type in the template and the number of returned reads for this DNA. We would argue that such a bias may be especially problematic in metabarcoding where samples usually contain trace DNA in unknown amounts. However, how this affects the completeness of metabarcoding results has yet been poorly investigated.

Eggshells as hosts of bacterial communities: An experimental test of the antimicrobial egg coloration hypothesis

Oviparous animals have evolved multiple defenses to prevent microbes from penetrating their eggs and causing embryo mortality. In birds, egg constituents such as lysozyme and antibodies defend against microbial infestation, but eggshell pigments might also impact survival of bacteria. If so, microbes could exert an important selective pressure on the evolution of eggshell coloration. In a previous lab experiment, eggshell protoporphyrin caused drastic mortality in cultures of Gram positive, but not Gram negative, bacteria when exposed to light. Here, we test this "photodynamic antimicrobial hypothesis" in a field experiment. In a paired experimental design, we placed sanitized brown, protoporphyrin-rich chicken eggs alongside white eggs that lack protoporphyrin. We deployed eggs for 48 hr without incubation, as can occur between laying and incubation, when microbial infection risk is highest. Eggs were placed on the open ground exposed to sunlight and in dark underground storm-petrel burrows. We predicted that the proportion of Gram-positive bacteria on brown eggs should be lower when exposed to sunlight than when kept in the dark, but we expected no such difference for white eggs. Although our data revealed variation in bacterial community composition, the proportion of Gram-positive bacteria on eggshells did not vary by egg color, and there was no interaction between egg color and location. Instead, Gram-positive bacteria were proportionally more common on eggs on the ground than eggs in burrows. Overall, our experiment did not support the photodynamic antimicrobial hypothesis. The diverse range of avian egg colors is generated by just two pigments, but over 10 hypotheses have been proposed for the evolution of eggshell color. If our results are generalizable, eggshell protoporphyrin might not play a substantial role in defending eggs against microbes, which narrows the field of candidate hypotheses for the evolution of avian eggshell coloration.

High-resolution multi-marker DNA metabarcoding reveals sexual dietary differentiation in a bird with minor dimorphism

Although sexual dietary differentiation is well known in birds, it is usually linked with significant morphological dimorphism between males and females, with lower differentiation reported in sexually monomorphic or only slightly dimorphic species. However, this may be an artifact of poor taxonomic resolution achieved in most conventional dietary studies, which may be unable to detect subtle intraspecific differentiation in prey consumption. Here, we show the power of multi‐marker metabarcoding to address these issues, focusing on a slightly dimorphic generalist passerine, the black wheatear Oenanthe leucura. Using markers from four genomic regions (18S, 16S, COI, and trnL), we analyzed fecal droppings collected from 93 adult black wheatears during the breeding season. We found that sexes were rather similar in bill and body features, though males had a slightly thicker bill and longer wings and tail than females. Diet was dominated in both sexes by a very wide range of arthropod species and a few fleshy fruits, but the overall diet diversity was higher for males than females, and there was a much higher frequency of occurrence of ants in female (58%) than male (29%) diets. We hypothesize that the observed sexual differentiation was likely related to females foraging closer to their offspring on abundant prey, while males consumed a wider variety of prey while foraging more widely. Overall, our results suggest that dietary sexual differentiation in birds may be more widespread than recognized at present and that multi‐marker DNA metabarcoding is a particularly powerful tool to unveiling such differences.