Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large-volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle Mesobot in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (~40-60 liters) samples collected by Mesobot with small volume (~2 liters) samples collected using the conventional CTD-mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume Mesobot and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not; although the number of unique taxa associated with the Mesobot samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.

Dataset of antiarch placoderms (the most basal jawed vertebrates) throughout Middle Paleozoic

Antiarch placoderms, the most basal jawed vertebrates, have the potential to enlighten the origin of the last common ancestor of jawed vertebrates. Quantitative study based on credible data is more convincing than qualitative study. To reveal the antiarch distribution in space and time, we created a comprehensive structured dataset of antiarchs comprising 64 genera and 6025 records. This dataset, which includes associated chronological and geographic information, has been digitalized from academic publications manually into the DeepBone database as a dateset. We implemented the paleogeographic map marker to visualize the biogeography of antiarchs. The comprehensive data of Antiarcha allow us to generate its biodiversity and variation rate changes throughout its duration. Structured data of antiarchs has tremendous research potential, including testing hypotheses in the fields of the biodiversity changes, distribution, differentiation,population and community composition. Also, it will be easily accessible by the other tools to generate new understanding on the evolution of early vertebrates. The data file described in this paper is available on https://doi.org/10.5281/zenodo.5639529 (Pan and Zhu, 2021).

Fungal biodiversity in Arctic paleoecosystems assessed by metabarcoding of lake sedimentary ancient DNA

Fungi are crucial organisms in most ecosystems as they exert ecological key functions and are closely associated with land plants. Fungal community changes may therefore help reveal biodiversity changes in past ecosystems. Lake sediments contain DNA of organisms in the catchment area, which allows reconstructing past biodiversity by using metabarcoding of ancient sedimentary DNA. We developed a novel PCR primer combination for fungal metabarcoding targeting a short amplicon to account for length bias of amplification due to ancient DNA degradation. In-silico PCRs showed higher diversity using this primer combination than using previously established fungal metabarcoding primers. We analyzed existing data from sediment cores from four artic and one boreal lake in Siberia. These cores had been stored for 2-22 years and examined degradation effects of ancient DNA and storage time-related bias in fungal communities. Amplicon size differed between fungal divisions, however, we observed no significant effect of sample age on amplicon length and GC content, suggesting robust results. We also found no indication of post-coring fungal growth during storage distorting ancient fungal communities. Terrestrial soil fungi, including mycorrhizal fungi and saprotrophs, were predominant in all lakes, which supports the use of lake sedimentary ancient DNA for reconstructing terrestrial communities.

A comprehensive assessment of the intertidal biodiversity along the Portuguese coast in the early 2000s

The unprecedented rates of current biodiversity loss have motivated a renewed interest in environmental and biodiversity monitoring. The need for sustained monitoring strategies has prompted not only the establisment of new long-term monitoring programmes, but also the rescue of data from historical or otherwise archived sources. Amongst the most valuable datasets are those containing information on intertidal systems, as they are particularly well suited for studying the biological effects of climate change. The Portuguese rocky coast is quite interesting for studying the effects of climate change on the distribution of species due to its geographical orientation, latitudinal patterns in temperature, species richness, species' distribution patterns and availability of historical information. This work aims at providing a comprehensive picture of the distribution and abundance of intertidal macro-invertebrates and macro-algae along the Portuguese rocky coast in the early 2000s. This study provides a description of the rocky shore intertidal biodiversity of the mainland Portuguese coast in the early 2000s. The spatial distribution and semi-quantitative abundance of a total of 238 taxa were assessed at 49 wave-exposed locations. These data provide a comprehensive baseline against which biodiversity changes can be effectively and objectively evaluated.

Diversity Scaling of Human Digestive Tract (DT) Microbiomes: The Intra-DT and Inter-individual Patterns

The human gut microbiome has been extensively studied, but its diversity scaling (changes or heterogeneities) along the digestive tract (DT) as well as their inter-individual heterogeneities have not been adequately addressed to the best of our knowledge. Here we fill the gap by applying the diversity-area relationship (DAR), a recent extension to the classic species-area relationship (SAR) in biogeography, by reanalyzing a dataset of over 2000 16s-rRNA microbiome samples obtained from 10 DT sites of over 200 individuals. We sketched out the biogeography “maps” for each of the 10 DT sites by cross-individual DAR analysis, and the intra-DT distribution pattern by cross-DT-site DAR analysis. Regarding the inter-individual biogeography, it was found that all DT sites have the invariant (constant) scaling parameter—all sites possessing the same diversity change rate across individuals, but most sites have different potential diversities, which include the portions of diversity that may be absent locally but present regionally. In the case of this study, the potential diversity of each DT site covers the total diversity of the respective site from all individuals in the cohort. In terms of the genus richness, an average individual hosts approximately 20% of the population-level genus richness (total bacterial genus of a human population). In contrast, in terms of community biodiversity, the percentages of individual over population may exceed 90%. This suggests that the differences between individuals in their DT microbiomes are predominantly in the composition of bacterial species, rather than how their abundances are distributed (i.e., biodiversity). Regarding the intra-DT patterns, the scaling parameter (z) is larger—suggesting that the intra-DT biodiversity changes are larger than inter-individual changes. The higher intra-DT heterogeneity of bacteria diversity, as suggested by larger intra-DT z than the inter-individual heterogeneity, should be expected since the intra-DT heterogeneity reflects the functional differentiations of the DT tract, while the inter-individual heterogeneity (z) reflects the difference of the same DT site across individuals. On average, each DT site contains 21–36% of the genus diversity of the whole DT, and the percentages are even higher in terms of higher taxon levels.

A REVIEW: IMPACT OF SOIL SALINITY ON ECOLOGICAL, AGRICULTURAL AND SOCIO-ECONOMIC CONCERNS

In recent years, salinization of soil is one of the challenging environmental concerns occurring all over the world. The effects of concentration of salt can be detected in both natural (primary) as well as man-made (secondary) environment. This is due to massive urbanization and industrialization in coastal regions, Soil salinity may lead to degradative changes in the composition of natural water resources, loss of fertile soil, loss of biodiversity, changes in local climatic conditions which in turn affects many aspects like, increasing salinization (salt affected soil) of lands converted in to non-productive conditions which significantly affects human life and posing major interruption to the economic development of farmers and their economy in the country. Furthermore, the overview of salinization and its effects on ecology, agriculture and economic growth and development is presented in this paper. Purpose of this review paper represented is according to most recent literature and refines knowledge on consistent research efforts for the types of soil salinity, problems of soil salinization, effect on plant growth and management strategies in agriculture to mitigate soil conditions in the salinity affected areas as well as rise in crop productivity and suggests future perspectives for on-going salinity research in the country.

Effect of Land Clearing Activity on Environmental and Arthropods Diversity (Case Study: Jati Agung, Lampung)

Agricultural activity relies on soil as their growth media. Besides agricultural activity, other living species also needs soil as their ecosystem. However, the biodiversity and environmental factor are often neglected in agricultural activity. Therefore, the investigation of environmental and biodiversity changes is important. In this study, the environmental parameter and biodiversity changes was investigated in area after land clearing activity. The pH was increased from in 3 times measurement. Besides, the soil temperature and air temperature was also increased in 3 times measurement between pre- and post-treatment. The soil temperature ranges from 26.2 oC to 33.2 oC in pre-treatment and 27.6 oC to 31.8 oC in post-treatment. The air temperature was observed ranges from 27.96 oC to 34.3 oC in pre-treatment and 28.36 oC to 34.56 oC in post-treatment. Measurement of RH was resulted ranges from 61.2% to 75.4% in pre-treatment and 61.4% to 74.8% in pre-treatment. The land is proposed become paddy field for next step land processing. As result, the diversity index was decreased in pre- and post-treatment. The Shannon diversity index was decreased from 0.81 to 0.72. Similarly, the Simpson diversity index was also decreased from 1.94 to 1.77. Meanwhile, the evenness index was increased from 0.58 to 0.65. These results suggested for farmer to process the land as soon as possible after land clearing process, if they want to form paddy field from pasture land.AbstrakKegiatan pertanian bergantung pada tanah sebagai media tumbuh suatu tanaman. Selain kegiatan pertanian, organisme hidup lain juga bergantung terhadap tanah sebagai ekosistem. Namun, seringkali biodiversitas dan faktor lingkungan diabaikan dalam kegiatan pertanian. Oleh karenanya, indentifikasi perubahan lingkungan dan biodiversitas sanget perlu dilakukan. Dalam penelitian ini, perubahan parameter lingkungan dan biodiversitas diamati sebelum dan sesudah aktivitas land clearing. Hasil pengamatan menunjukkan, pH tanah, suhu tanah dan suhu lingkungan meningkat dalam 3 kali pengukuran dari sebelum ke sesudah aktivitas land clearing. Suhu tanah berkisar 26.2 oC-33.2 oC pada sebelum kegiatan land clearing dan 27.6 oC-31.8 oC setelah aktivitas land clearing. Suhu lingkungan ditemukan berkisar 27.96 oC-34.3 oC pada kegiatan sebelum land clearing dan 28.36 oC-34.56 oC setelah kegiatan land clearing. Hasil pengukuran RH lingkungan ditemukan berkisar 61.2%-75.4% pada kegiatan sebelum land clearing dan 61.4%-74.8% setelah kegiatan land clearing. Sementara itu, index diversitas ditemukan menurun setelah aktivitas land clearing. Nilai Shannon diversity index ditemukan menurun setelah aktivitas land clearing dari 0.81-0.72. Pola serupa ditemukan pada nilai Simpson diversity index, dimana terjadi penurunan dari 1.94 menjadi 1.77. Nilai evenness index meningkat dari 0.58 menjadi 0.65. Berdasarkan hasil tersebut dapat disarankan ke petani untuk segera mengolah lahan tersebut setelah kegiatan land clearing untuk menghindari terjadinya pertumbuhan kembali vegetasi, serta perubahan parameter lingkungan dan biodiversitas.

Managing human mediated range shifts: understanding spatial, temporal and genetic variation in marine non- native species

The use of molecular methods to manage natural resources is increasingly common. However, DNA-based methods are seldom used to understand the spatial and temporal dynamics of species' range shifts. This is important when managing range-shifting species such as non-native species (NNS), which can have negative impacts on biotic communities. Here we investigated the range-shifting NNS Ciona robusta, Clavelina lepadiformis, Microcosmus squamiger and Styela plicata using a combined methodological approach. We first conducted non-molecular biodiversity surveys for these NSS along the South African coastline, and compared the results with historical surveys. We detected no consistent change in range size across species, with some displaying range stability and others showing range shifts. We then sequenced a section of cytochrome c oxidase subunit I (COI) from tissue samples and found genetic differences along the coastline but no change over recent times. Finally, we found that environmental DNA metabarcoding data showed broad congruence with both the non-molecular biodiversity and the COI datasets, but failed to capture complete incidence of all NSS. Overall, we demonstrated how a combined methodological approach can effectively detect spatial and temporal variation in genetic composition and range size, which is key for managing biodiversity changes of both threatened and NSS.