Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline

Fungal communities associated with plants and soil influence plant fitness and ecosystem functioning. They are frequently studied by metabarcoding approaches targeting the ribosomal internal transcribed spacer (ITS), but there is no consensus concerning the most appropriate bioinformatic approach for the analysis of these data. We sequenced an artificial fungal community composed of 189 strains covering a wide range of Ascomycota and Basidiomycota, to compare the performance of 360 software and parameter combinations. The most sensitive approaches, based on the USEARCH and VSEARCH clustering algorithms, detected almost all fungal strains but greatly overestimated the total number of strains. By contrast, approaches using DADA2 to detect amplicon sequence variants were the most effective for recovering the richness and composition of the fungal community. Our results suggest that analyzing single forward (R1) sequences with DADA2 and no filter other than the removal of low-quality and chimeric sequences is a good option for fungal community characterization.     

Functional diversity across space and time: trends in wader communities on British estuaries

Aim British estuarine ecosystems support large populations of protected migratory waders. Understanding how wader communities vary spatially and how they may be changing temporally can greatly improve the understanding of these dynamic ecosystems. Here, we explore the variation in functional diversity (using a range of morphological and ecological traits) in order to identify the processes shaping wader communities on British estuaries and how these processes may be changing. Location England, Wales and Scotland. Methods We use national survey data (Wetland Bird Survey) from 1980/1981 to 2006/2007 winter to calculate functional diversity (FD) – an index that measures trait dispersion – in wader communities on 100 estuaries. We test for evidence of non‐random patterns of diversity and explore the relative importance of two key processes, environmental filtering and competition, in shaping these communities. Results The observed FD was significantly and positively associated with species richness and to a lesser extent estuary area, followed by longitude. An increase in observed FD was observed since 1980, supported by a small but significant slope. In the majority of cases, changes in FD were mirrored by changes in species richness. Observed FD was on average lower than expected by chance, as indicated by a negative value of observed minus expected FD. However, this difference became less negative over time, with observed minus expected FD values increasing slightly, but significantly, over the study period. Main conclusions Wader FD varies across British estuaries, and the relative influence of the processes by which communities are structured appears to be changing through time. We discuss the potential drivers underlying these patterns and the importance of identifying such drivers for the protection of wader communities.     

乌鲁木齐市小型兽类群落特征与分布格局初步研究

根据2002年7月的调查资料对乌鲁木齐市养禽场鼠类群落进行了研究。结果表明：该地区分布的鼠类可划分为2种群落,(1)褐家鼠 小家鼠群落;(2)小家鼠 灰仓鼠群落。同时对鼠类群落的多样性,均匀度等进行了初步研究。     

A comparative analysis of metabarcoding and morphology‐based identification of benthic communities across different regional seas

In a world of declining biodiversity, monitoring is becoming crucial. Molecular methods, such as metabarcoding, have the potential to rapidly expand our knowledge of biodiversity, supporting assessment, management, and conservation. In the marine environment, where hard substrata are more difficult to access than soft bottoms for quantitative ecological studies, Artificial Substrate Units (ASUs) allow for standardized sampling. We deployed ASUs within five regional seas (Baltic Sea, Northeast Atlantic Ocean, Mediterranean Sea, Black Sea, and Red Sea) for 12–26 months to measure the diversity and community composition of macroinvertebrates. We identified invertebrates using a traditional approach based on morphological characters, and by metabarcoding of the mitochondrial cytochrome oxidase I (COI) gene. We compared community composition and diversity metrics obtained using the two methods. Diversity was significantly correlated between data types. Metabarcoding of ASUs allowed for robust comparisons of community composition and diversity, but not all groups were successfully sequenced. All locations were significantly different in taxonomic composition as measured with both kinds of data. We recovered previously known regional biogeographical patterns in both datasets (e.g., low species diversity in the Black and Baltic Seas, affinity between the Bay of Biscay and the Mediterranean). We conclude that the two approaches provide complementary information and that metabarcoding shows great promise for marine monitoring. However, until its pitfalls are addressed, the use of metabarcoding in monitoring of rocky benthic assemblages should be used in addition to classical approaches rather than instead of them.     

A new diagnostic approach to fast-track and increase the accessibility of gastrointestinal nematode identification from faeces: FECPAKG2 egg nemabiome metabarcoding

Effective gastrointestinal nematode management in livestock industries is becoming increasingly difficult due to the rise of anthelmintic resistance and changes in the temporal and geographical distribution of major gastrointestinal nematodes. Underpinning the response to these challenges is the need for a fast-tracked diagnostic identification technique, making it easier for livestock producers to make informed gastrointestinal nematode management decisions. The traditional ‘gold-standard’ approach, larval culture followed by morphological differentiation, is laborious and potentially inaccurate. We developed a new diagnostic approach to identify gastrointestinal nematodes that integrates a remote-location digital faecal egg count platform, FECPAK^G2, with internal transcribed spacer 2 (ITS2) nemabiome metabarcoding. The technique involves a quick and simple protocol to harvest concentrated strongyle eggs from the FECPAK^G2 cassette utilising a repurposed pipette tip, followed by DNA isolation and Illumina next generation amplicon sequencing. The gastrointestinal nematode compositions and alpha diversity generated by our FECPAK^G2 egg nemabiome metabarcoding approach was not significantly different to traditional morphological larval differentiation and nemabiome metabarcoding of larval and faecal samples. We demonstrated that storing FECPAK^G2 harvested eggs in either DNA isolation lysis buffer or 80% ethanol (v/v) had no impact on gastrointestinal nematode identification outcomes for at least 60 days; enabling the transport of biological samples from their remote origins to a molecular diagnostic facility for nemabiome metabarcoding, in the absence of a cold chain. We discovered that sustained gastrointestinal nematode egg embryonation in the lysis buffer storage solution lead to higher yields of DNA compared with ethanol-stored gastrointestinal nematode eggs or faeces with gastrointestinal nematode eggs. Taking advantage of an already well-established platform such as FECPAK^G2, and providing the livestock producers that use it with the option to identify gastrointestinal nematodesin their samples and contribute to large-scale gastrointestinal nematode distribution and/or anthelmintic resistance surveys, is an important future direction for the FECPAK^G2 egg nemabiome metabarcoding approach.     

Historical DNA as a tool to address key questions in avian biology and evolution: A review of methods,challenges, applications,and future directions

Museum specimens play a crucial role in addressing key questions in systematics, evolution, ecology, and conservation. With the advent of high‐throughput sequencing technologies, specimens that have long been the foundation of important biological discoveries can inform new perspectives as sources of genomic data. Despite the many possibilities associated with analyzing DNA from historical specimens, several challenges persist. Using avian systems as a model, we review DNA extraction protocols, sequencing technologies, and capture methods that are helping researchers overcome some of these difficulties. We highlight empirical examples in which researchers have used these technologies to address fundamental questions related to avian conservation and evolution. Increasing accessibility to new sequencing technologies will provide researchers with tools to tap into the wealth of information contained within our valuable natural history collections.     

Subsurface-flow constructed wetlands in Spain for the sanitation of small communities: A comparative study

In comparison with other European countries, constructed wetlands may still be considered a recent technology in Spain. A survey of the systems treating urban wastewater in this country revealed that over 80% of subsurface-flow constructed wetlands have been built over the last 5 years, horizontal systems (HF-CW) alone or in combination with other unit processes such as ponds being the most widespread type. Organic loads ranged from 0.8 to 23, from 22.8 to 29.8 and from 3.6 to 16.7 g BOD m⁻² day⁻¹ for HF-CW (alone), vertical systems (VF-CW) and combined systems (HF-CW with other unit processes), respectively. The performance of such systems in terms of BOD₅ removal generally ranged from 80 to 95% in all cases (HF-CW, VF-CW and combined systems), whereas COD removal was slightly lower, ranging from 50 to 95%, 80 to 95% and 50 to 90% for the HF-CW, VF-CW and combined systems, respectively. Furthermore, the TSS removal rate ranged from 70 to 95% for combined systems and from 85 to 95% for HF-CW (alone). The systems were not very efficient in terms of nutrient removal (nitrogen and phosphorus), with total average removal efficiencies around 40–50%. In general terms, the analysis of constructed wetlands in Spain shows that although they operate with higher loads than in other European systems, their performance in terms of organic matter and nutrient removal is in the range of that described in previous studies.     

Reusable biotelemetric capsules: A convenient and reliable method for measuring core body temperature in large mammals during gut passage

It is still not fully understood how megaherbivores regulate their body temperature (T_b), particularly with respect to their unfavourable surface to volume ratio. The paucity of information is probably owing to the difficulty obtaining physiological parameters from such animals. We developed a precise and reliable non-invasive method for determining the T_b of large-bodied mammals. We used this method on African and Asian elephants. Small capsules (30 g) containing a temperature-sensitive transmitter and a memory for onboard data storage were hand-fed 71 times to elephants (N=21) and T_b was measured during gut passage. In 64 cases, sensors were successfully retrieved. The operation and reliability of our data loggers was sufficient and compared favourably with any other published method.     

A novel method of characterizing genetic sequences: genome space with biological distance and applications

Background

Most existing methods for phylogenetic analysis involve developing an evolutionary model and then using some type of computational algorithm to perform multiple sequence alignment. There are two problems with this approach: (1) different evolutionary models can lead to different results, and (2) the computation time required for multiple alignments makes it impossible to analyse the phylogeny of a whole genome. This motivates us to create a new approach to characterize genetic sequences.

Methodology

To each DNA sequence, we associate a natural vector based on the distributions of nucleotides. This produces a one-to-one correspondence between the DNA sequence and its natural vector. We define the distance between two DNA sequences to be the distance between their associated natural vectors. This creates a genome space with a biological distance which makes global comparison of genomes with same topology possible. We use our proposed method to analyze the genomes of the new influenza A (H1N1) virus, human rhinoviruses (HRV) and mammalian mitochondrial. The result shows that a triple-reassortant swine virus circulating in North America and the Eurasian swine virus belong to the lineage of the influenza A (H1N1) virus. For the HRV and mammalian mitochondrial genomes, the results coincide with biologists'' analyses.

Conclusions

Our approach provides a powerful new tool for analyzing and annotating genomes and their phylogenetic relationships. Whole or partial genomes can be handled more easily and more quickly than using multiple alignment methods. Once a genome space has been constructed, it can be stored in a database. There is no need to reconstruct the genome space for subsequent applications, whereas in multiple alignment methods, realignment is needed to add new sequences. Furthermore, one can make a global comparison of all genomes simultaneously, which no other existing method can achieve.     

A taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter

The genus Prevotella comprises 55 species with validly published, and correct, names (at June 2021) that are phenotypically, ecologically and functionally diverse. This study used a range of comparative genome approaches (marker gene-based genome phylogeny, core genome phylogeny, average amino acid identity, percentage of conserved proteins and clade-specific marker genes) to identify large differences between the 53 species for which genomes are available, as well as two effectively published yet not validly named species and four novel species. These differences were consistent between the various analysis methods and justify the separation of Prevotella into multiple genera. While the distribution across 19 ecosystem types was unique for each species and inconsistent within clades, the functional repertoire based on the presence/absence of both PFAMs and CAZy families revealed distinct clustering based on the proposed genera. Based on the integration of all results, we propose the reclassification of species previously assigned to the genus Prevotella into seven genera, including four novel genera for which the names Segatella, Hoylesella, Leyella and Palleniella are proposed. In addition to the reclassification of Prevotella, this work describes four novel species, Hallella faecis, Xylanibacter rodentium, Xylanibacter muris, and Palleniella intestinalis.     

Nested communities,invasive species and Holocene extinctions: evaluating the power of a potential conservation tool

General ecological methods and models that require a minimum amount of information yet are still able to inform conservation planning are particularly valuable. Nested subset analysis has been advocated as such a tool for the prediction of extinction-prone species and populations. However, such advocacy has not been without skepticism and debate, and in the majority of published examples assessing extinction vulnerability, actual extinctions are based on assumptions rather than direct evidence. Here, we empirically test the power of nested subset analysis to predict extinction-prone species, using documented Holocene insular mammal extinctions on three island archipelagos off the west coast of North America. We go on to test whether the introduction of invasive mammals promotes nestedness on islands via extinction. While all three archipelagos were significantly nested before and after the extinction events, nested subset analysis largely failed to predict extinction patterns. We also failed to detect any correlations between the degree of nestedness at the genus-level with area, isolation, or species richness and extinction risk. Biogeography tools, such as nested subset analysis, must be critically evaluated before they are prescribed widely for conservation planning. For these island archipelagos, it appears detailed natural history and taxa-specific ecology may prove critical in predicting patterns of extinction risk.     

Plant invasion across space and time: factors affecting nonindigenous species success during four stages of invasion

Invasive nonindigenous plant species (NIPS) threaten native diversity, alter ecosystem processes, and may interact with other components of global environmental change. Here, a general framework is outlined that attempts to connect patterns of plant invasion to processes underlying these patterns at four well-established spatio-temporal stages of the invasion process: transport, colonization, establishment, and landscape spread. At each stage we organize findings and ideas about the filters that limit NIPS success and the interaction of these filters with historical aspects of introduction events, NIPS traits, and ecosystem properties. While it remains difficult to draw conclusions about the risk of invasion across ecosystems, to delineate universal 'invader traits', or to predict large-scale extinctions following invasions, this review highlights the growing body of research that suggests that the success of invasive NIPS is controlled by a series of key processes or filters. These filters are common to all invasion events, and will interact throughout the stages of plant invasion, although the relative importance of a filter may be stage, species or location specific. It is suggested that both research and management programs may benefit from employing multiscale and stage approaches to studying and controlling invasion. We further use the framework to briefly examine potential interactions between climate change and filters that limit NIPS invasion.     

The historical bridge between the Amazon and the Atlantic Forest of Brazil: a study of molecular phylogeography with small mammals

Abstract Aim To examine how the genetic diversity of selected taxa of forest‐dwelling small mammals is distributed between and within the major rain forest domains of Amazonia and Atlantic Forest and the intervening interior forests of Brazil, as inferred by the relationships between gene genealogies and geography. I also addressed the historical importance of the central Brazilian forests in connecting Amazon and Atlantic Forest populations of rodents and marsupials. Methods I evaluated variation in the mitochondrial cytochrome b gene to estimate the levels of sequence divergence between those taxa occurring throughout the Amazon, Atlantic Forest, and forests in the Cerrado and Caatinga regions. I inferred the hierarchical relationships between haplotypes, populations and formal taxa using the cladistic approach of maximum parsimony. I compared areas and the clades identified by superimposing cladograms on the geographical distribution of samples. The degree of concordance both in phylogeny and the depth of the nodes in these phylogenies, in addition to patterns of geographical distribution of clades, permitted me to make inferences on how, when and where the taxa differentiated. Results Sequence similarity is often greater between samples from the Atlantic Forest and either Amazon or central Brazilian forests than it is within each of the two rain forest domains. The Atlantic Forest clades are either not reciprocally monophyletic or are the sister group to all the other clades. There is some indication of northern and southern components in the Atlantic Forest. Given the geographical distribution of clades and the relatively deep levels of divergence, the central Brazilian area does not behave as a separate region but is complementary to either Amazon or Atlantic Forest. Patterns of area relationships differ across taxa, suggesting that different processes and/or historic events affected the diversification within each lineage. Main conclusions The Amazon and the Atlantic forests are not exclusive in terms of their small mammal faunas; both overlap broadly with taxa occurring in gallery forests and dry forests in central Brazil. Central Brazilian forests are an integral part of the evolutionary scenario of lowland small mammals, playing an important role as present and past habitats for rain forest species. Therefore, representatives from this area should always be included in analyses of the evolutionary history of lowland rain forest faunas. The incongruence of branching patterns among areas is in agreement with recent results presented for Neotropical passerine birds and indicates that a single hypothesis of Neotropical area relationships is unlikely. These findings reinforce the idea that speciation in the Neotropics will not be explained by any single model of vicariance or climatic changes.     

Enriching the biological space of natural products and charting drug metabolites,through real time biotransformation monitoring: The NMR tube bioreactor

Background

Natural products offer a wide range of biological activities, but they are not easily integrated in the drug discovery pipeline, because of their inherent scaffold intricacy and the associated complexity in their synthetic chemistry. Enzymes may be used to perform regioselective and stereoselective incorporation of functional groups in the natural product core, avoiding harsh reaction conditions, several protection/deprotection and purification steps.

A simple and novel method for recovering adenovirus 41 in small volumes of source water

Aim: A new procedure was developed to recover adenovirus 41 in small volumes (1 l) of water samples based on adsorption, elution and evaporation. Methods and Results: One litre of source water seeded with adenovirus 41 was adjusted to pH 3·5 and filtered using a large pore size (8·0 μm) negatively charged membrane filter (SCWP, 47 mm diameter, made of mixed‐cellulose esters). Then, the filter was eluted using 4 ml of 1·5% beef extract plus 0·75% glycerol (pH 9·0). The eluate was reconcentrated to 0·1 ml or less volumes through evaporation assisted with air flow and heating at 55°C. Recovery of adenovirus 41 reached 55% under tested conditions and reduced filtration time by 85% in contrast to the widely used small pore size filter (0·45 μm pore size, 47 mm diameter). Reconcentration by evaporation achieved approx. 86·8% recovery from source water in approx. 1 h at no cost. Conclusion: The virus concentration method developed in this study is simple and cost‐effective and can be used to efficiently recover adenovirus 41 from turbid water samples. Significance and Impact of the Study: The procedure developed can be applied to detect adenovirus 41 in source water within hours of sampling. In addition, this is the first application of evaporation to concentrate viruses in water samples.     

Influence of climate changes on animal communities in space and time: the case of spider assemblages along an alpine glacier foreland

The impact of global warming in space and time is described for species assemblages of wandering spiders along the alpine glacier foreland of the Forni Valley (Northern Italy). We tested the effect of environmental variables (e.g. elevation, age of glacier retreat, vegetation cover, debris cover) on species richness and on species composition of spiders. Age of glacier retreat was the only significant variable influencing spider species assemblages in the valley. A spatially structured distribution of species and species assemblages along the chronosequence of glacier retreat was evidenced. The threshold abruptly differentiating two groups of species richness and species composition fell between sites deglaciated 100 and 155 years before the analysis. Latitudinal shifts towards the poles in species ranges at the global scale in response to climatic changes are known, and an altitudinal shift in species range should be expected for spiders at the local scale of the Forni Valley. Such a shift is present in spider species assemblages, although not as an expected gradual change in species richness and composition, but with a threshold effect after one century of glacier retreat. We discuss our results in the light of plausible future scenarios due to global warming, the consequence of further glacier retreats onto spiders, and caveats for monitoring studies.