Genus Richness Research Articles

Spruce girdling decreases abundance of fungivorous soil nematodes in a boreal forest

The relative importance of belowground and aboveground energy inputs for the decomposer communities in soil remains largely unknown. In particular, no research has been done on the significance of root-derived resources for nematode communities in boreal forests. In two spruce stands in the taiga zone, we set up a field experiment in which girdling of spruce trees and clipping of dwarf shrubs was performed. Root-derived resources were hypothesized to be highly important; accordingly, we expected to observe a suppression of the nematode community after experimental manipulations. To obtain information on the nature of changes in the soil food web, nematode community structure indices were applied. In partial confirmation of our hypothesis, spruce girdling decreased mycorrhizal hyphae biomass as assessed via in-growth mesh bags, as well as the abundance of fungivorous nematodes, mostly of the Aphelenchoides and Filenchus genera. The enrichment index (EI) value decreased, indicating reduction of organic matter inputs into the soil food web, whereas nematode channel ratio (NCR) index value increased, indicating a shift towards domination of the bacterial energy channel. Total nematode abundance, genera richness, and abundance of herbivores, omnivores, and predators did not change in response to spruce girdling. Clipping of dwarf shrubs decreased fungal and bacterial PLFA biomarkers, but did not affect nematode communities. Thus, the resources channeled in soil by the roots of canopy trees are of different relative importance for nematodes having different trophic habits. Fungivorous nematodes are at least partly dependent on root-derived resources, suggesting feeding on ectomycorrhizal mycelium. Rhizodeposits of understory vegetation are likely of low importance for nematodes.

Diversity, distribution, and classification of Neotropical woody bamboos (Poaceae: Bambusoideae) in the 21st Century

Background: The Neotropical woody bamboos (NWB) comprise a clade native to the Western Hemisphere. Taxonomically the NWB are classified into three subtribes: Arthrostylidiinae, Chusqueinae, and Guaduinae. These woody bamboos are distributed from northern Mexico and the West Indies to south-central Chile and Argentina and from sea level to over 4,000 m in elevation. The most recent comprehensive treatment of the diversity and classification of NWB was published just over 20 years ago, and knowledge of the NWB has greatly increased in the interim.
 Questions and / or Hypotheses: How much has our knowledge of Neotropical woody bamboo diversity, distribution and classification changed in the last 20 years?
 Results: The present work reviews the current state of Neotropical woody bamboo taxonomy and provides 1) new morphological keys (in English and Spanish) to and synoptic descriptions of the NWB genera; 2) an updated comprehensive species list; and 3) a biodiversity analysis by country and habitat type. Neotropical woody bamboo diversity presently totals 446 species in 23 genera. In the 21st century, 103 new species and five genera of NWB have been described.
 Conclusions: The new species and genera described since 2000 have produced an increase in species richness of 29.5 % and a net increase in generic richness of 26.3 %. This new review will be useful for systematists, ecologists, conservation biologists and others working with woody bamboos in the Neotropics.

Deep-Sea Nematodes of the Mozambique Channel: Evidence of Random Community Assembly Dynamics in Seep Sediments

Cold seeps occur globally in areas where gases escape from the seafloor, occasionally resulting in the formation of topographic depressions (pockmarks), characterised by unique physicochemical conditions such as anoxic and sulphuric sediments. Free-living marine nematodes tend to dominate the meiofaunal component in such environments, often occurring at extremely high densities and low richness; the mechanisms defining community assembly in areas of fluid seepage, however, have received little attention. Here we focus on a low-activity pockmark at 789 m in the Mozambique Channel (MC). We assessed the diversity, co-occurrence patterns and phylogenetic community structure of nematodes at this bathyal site to that of a nearby reference area as well as abyssal sediments using metabarcoding. In addition, we compared our molecularly-derived diversity estimates to replicate samples identified morphologically. Overall, nematode Amplicon Sequence Variants (ASVs) and generic richness were similar between Pockmark and Abyssal sediments, but lower compared to the Reference area. Although more than half the genera were shared, over 80% of ASVs were unique within each area and even within each replicate core. Even though both methodologies differentiated the Pockmark from the Reference and Abyssal sites, there was little overlap between the molecularly and morphologically identified taxa, highlighting the deficit of reference sequences for deep-sea nematodes in public databases. Phylogenetic community structure at higher taxonomic levels was clustered and did not differ between the three areas yet analysis within three shared and dominant genera (Acantholaimus, Desmoscolex, Halalaimus), revealed randomness with respect to phylogeny as well as co-occurrence which was exclusive to the Pockmark area. These patterns point to the influence of neutral dynamics at this locality resulting from the stochastic sampling of early colonizing taxa, the successional stage at sampling and/or the functional redundancy within the investigated genera.

Effects of different carbon inputs on soil nematode abundance and community composition

Plants provide carbon (C) input to the soil and energy resources for soil food webs through litter and roots. However, it remains uncertain which C input pathway is more important and how different C inputs affect the community composition of the soil fauna. A long-term (9 years) field C input manipulation experiment was conducted to investigate the effects of C inputs on soil nematodes. Plant removal, litter addition, and litter removal were carried out to simulate changes in below- and aboveground C inputs. Results showed that plant removal significantly decreased soil resource availability (i.e., the soil organic C and total nitrogen). Plant removal also decreased nematode abundance (73.09%) and genus richness (17.98%). The relative abundance of bacterivores was enhanced but plant parasites and omnivores-predators were reduced by plant removal. The significantly lower soil pH and higher NO3−-N concentrations under the plant removal treatment are probably responsible for changing the community structure. Litter addition increased nematode abundance by 37.88%, but litter removal decreased the genus richness by 9.39%. There were significant interactive effects of plant removal and litter manipulation on the total nematode abundance and genus richness. Our observations suggest that belowground C input has greater impacts on soil nematodes than the above-ground C input, and that the impacts of litter on the soil nematode community could be mediated by living plants.

Analysis of global human gut metagenomes shows that metabolic resilience potential for short-chain fatty acid production is strongly influenced by lifestyle

High taxonomic diversity in non-industrial human gut microbiomes is often interpreted as beneficial; however, it is unclear if taxonomic diversity engenders ecological resilience (i.e. community stability and metabolic continuity). We estimate resilience through genus and species-level richness, phylogenetic diversity, and evenness in short-chain fatty acid (SCFA) production among a global gut metagenome panel of 12 populations (n = 451) representing industrial and non-industrial lifestyles, including novel metagenomic data from Burkina Faso (n = 90). We observe significantly higher genus-level resilience in non-industrial populations, while SCFA production in industrial populations is driven by a few phylogenetically closely related species (belonging to Bacteroides and Clostridium), meaning industrial microbiomes have low resilience potential. Additionally, database bias obfuscates resilience estimates, as we were 2–5 times more likely to identify SCFA-encoding species in industrial microbiomes compared to non-industrial. Overall, we find high phylogenetic diversity, richness, and evenness of bacteria encoding SCFAs in non-industrial gut microbiomes, signaling high potential for resilience in SCFA production, despite database biases that limit metagenomic analysis of non-industrial populations.

Occupancy models reveal regional differences in detectability and improve relative abundance estimations in fossil pollen assemblages

The late Quaternary fossil record provides crucial data that demonstrate how organisms respond to climate change. These records have been used to great effect, demonstrating that no-analog communities frequently occur during periods of no-analog climate, and that taxa demonstrate individualistic responses to change. However, our efforts to reconstruct biotic responses to environmental change are frequently hampered by inconsistent sampling and differential preservation of fossil taxa. We leveraged occupancy modeling methods and the fossil pollen record across eastern North America to identify circumstances under which occupancy modeling improves our ability to estimate relative abundance in four pollen taxa (Cornus, Fagus, Picea, and Pinus) through time (15 kya to present) and to identify localities where data are unreliable reflections of the local community. We found that integrating observed pollen abundance and detectability improves model performance. Low genus richness and large basin area were consistently important determinants of low detection. Our occupancy models were most informative for taxa with high enough variation in observed pollen abundance for models to be adequately calibrated. We combined occupancy model estimates of pollen abundance and detectability with a Getis-Ord statistical approach to identify spatial clusters of high or low detectability, identifying regions where a taxon’s pollen is more (or less) reliable. This work will advance the integration of ecological and paleontological sciences by allowing us to better identify whether a pollen taxon is truly absent from a fossil site or if it has simply gone undetected, allowing us to produce more robust paleoecological models. This approach will bolster our ability to identify the responses of plant communities to past climatic and anthropogenic change so that we can improve our predictions of future responses.

Geographical and temporal patterns of cyanobacterial assemblages in the Danube Delta lake complexes

Danube Delta shallow lakes experience cyanobacteria blooms that can negatively affect the aquatic ecosystem. Although there are several studies on Danube Delta cyanobacteria, little is known about their spatial–temporal patterns and the potential predictive role they can offer. We therefore analyzed the distribution of cyanobacteria in 19 lakes belonging to three lake complexes and tested whether their seasonal dynamics are in line with the predictions of the PEG model. Furthermore, we investigated to which extent cyanobacteria diversity and abundance were related to lake hydrogeomorphological characteristics such as surface, water level, connectivity, water retention, flood risk, and transparency. Although lakes had different seasonal cyanobacterial assemblages, the biovolume and genus richness had a geographical pattern, decreasing from south-east (lakes forming the fluvial delta) towards north-west (lakes forming the maritime delta). Cyanobacteria biovolume reflected largely the PEG model peaking in summer (the fluvial delta) and autumn (the maritime delta). Genus richness followed the same pattern. Cyanobacteria distribution was predicted by various abiotic (e.g., risk of flooding, connectivity) and biotic factors (e.g., submersed macrophytes, phytoplankton diversity, peat deposits). Our study contributes to the understanding of cyanobacteria diversity and distribution in shallow interconnected lakes by revealing the complexity of predictors for geographical and seasonal patterns.

Re-establishment of nematode communities in a rehabilitated surface mining area in Sibutad, southern Philippines

Ore mineral extraction involves stripping of topsoils that can lead to eradication of soil biota, including nematodes. Hence, rehabilitation is needed to assist in the recovery of damaged soil ecosystems. In many developing countries, e.g., the Philippines, rehabilitation of soils is mostly carried out through addition of organic amendments and development of aboveground vegetation. Rehabilitation success is often judged based on the survival or growth rate of plants, (e.g., Acacia sp.). This may not be sufficient since tree species used for rehabilitation can tolerate harsh soil conditions. In the present study, we instead examined the response of soil nematodes that are often considered the most abundant soil taxa and play important roles in soil functioning. We assessed the re-establishment of nematode communities in ‘rehabilitated’ areas between 8 and 13 years after the onset of their rehabilitation by comparing nematode community descriptors (e.g., abundance, evenness and diversity indices) and genus composition of four different sites (three rehabilitated and one reference) between two time periods (2012 vs. 2014). Nematodes were collected in 2012 and 2014, and identified to the genus level using a traditional approach (morphology-based identification). Results show that despite the development of vegetation, there was an overall low abundance in all of the sampling sites in Sibutad probably due to a naturally extremely acidic soil pH in the area. Hints of recovery of nematode communities, however, were manifested by the increase in nematode abundance and genus richness, and by the appearance of ‘sensitive’ nematode genera in rehabilitated areas after two additional years of rehabilitation. Using the 2012 data, our results show that high Pb concentrations and a lack of organic matter in the topsoils influenced nematode genus composition; this can provide valuable information for the optimization of rehabilitation measures for disturbed soils.

Phytoplankton Community Response to Nutrients, Temperatures, and a Heat Wave in Shallow Lakes: An Experimental Approach

Phytoplankton usually responds directly and fast to environmental fluctuations, making them useful indicators of lake ecosystem changes caused by various stressors. Here, we examined the phytoplankton community composition before, during, and after a simulated 1-month heat wave in a mesocosm facility in Silkeborg, Denmark. The experiment was conducted over three contrasting temperature scenarios (ambient (A0), Intergovernmental Panel on Climate Change A2 scenario (circa +3 °C, A2) and A2+ %50 (circa +4.5 °C, A2+)) crossed with two nutrient levels (low (LN) and high (HN)) with four replicates. The facility includes 24 mesocosms mimicking shallow lakes, which at the time of our experiment had run without interruption for 11 years. The 1-month heat wave effect was simulated by increasing the temperature by 5 °C (1 July to 1 August) in A2 and A2+, while A0 was not additionally heated. Throughout the study, HN treatments were mostly dominated by Cyanobacteria, whereas LN treatments were richer in genera and mostly dominated by Chlorophyta. Linear mixed model analyses revealed that high nutrient conditions were the most important structuring factor, which, regardless of temperature treatments and heat waves, increased total phytoplankton, Chlorophyta, Bacillariophyta, and Cyanobacteria biomasses and decreased genus richness and the grazing pressure of zooplankton. The effect of temperature was, however, modest. The effect of warming on the phytoplankton community was not significant before the heat wave, yet during the heat wave it became significant, especially in LN-A2+, and negative interaction effects between nutrient and A2+ warming were recorded. These warming effects continued after the heat wave, as also evidenced by Co-inertia analyses. In contrast to the prevailing theory stating that more diverse ecosystems would be more stable, HN were less affected by the heat wave disturbance, most likely because the dominant phytoplankton group cyanobacteria is adapted to high nutrient conditions and also benefits from increased temperature. We did not find any significant change in phytoplankton size diversity, but size evenness decreased in HN as a result of an increase in the smallest and largest size classes simultaneously. We conclude that the phytoplankton community was most strongly affected by the nutrient level, but less sensitive to changes in both temperature treatments and the heat wave simulation in these systems, which have been adapted for a long time to different temperatures. Moreover, the temperature and heat wave effects were observed mostly in LN systems, indicating that the sensitivity of phytoplankton community structure to high temperatures is dependent on nutrient availability.

PSIV-19 Relationship between liver abscess microbiome of feedlot cattle and soil organic matter microbiome isolated from feedlot pens

Abstract Liver abscess (LA) prevalence has increased 15% for beef cattle and 25% for Holstein cattle. The prevalence of liver abscesses in the Central Plains region (CR) is greater than the Southwest region (SR) of the United States. The objective was to evaluate soil organic matter (SOM) microbiome of feedlot pens, associated LA microbiomes, and the impact of breed, location, and tylosin. Eighty-three commercial feedlot pens were sampled for SOM prior to harvesting and LA samples were collected from two commercial packing plants in Tolleson, AZ (SR) and Greely, CO (CR). Liver abscess samples were linked to SOM samples. Amplification and sequencing of the V4 variable region of the 16S rRNA gene was performed using the Illumina MiSeq. Bacterial phyla, genera, and diversity indices were reported for LA and SOM samples. Reported data is from a subset of five pens. The most prevalent genera identified in liver abscesses were Fusobacterium (64.2%) and Bacteroides (18.6%). Predominant SOM genera were Atopostipes (13%) and Clostridium (10%). Phylum SOM Shannon Weiner Index (SWI) was lower for the CR compared to the SR (0.034 vs. 0.174; P < 0.05), indicating a dominant bacterium in the CR. Atopostipes and Clostridium comprised 48% of the CR SOM, explaining the lower SWI. The SWI of SOM and liver abscesses of Holsteins are lower (P < 0.05) compared to beef counterparts. Additionally, Clostridium, Fusobacterium, and Atopostipes populations were greater (P < 0.05) in SOM of Holstein pens than beef pens. Genus richness was lower (P < 0.05) for both SOM and liver abscesses from pens of cattle fed tylosin vs. no tylosin. There is a negative correlation between SOM SWI and LA% (R2 = -0.49; P = 0.03) and LA severity (A+) (R2 = -0.44; P = 0.05). In conclusion, SOM may serve as a potential vector for liver abscesses.

Do spatial and temporal scales affect the efficiency of surrogates in ant monitoring on the hydroelectric power-plant area in Brazilian Amazon?

In the last decade, we have experienced a huge loss of biodiversity on the planet. One of the possible ways to overcome this loss is to focus on places of human interest, monitoring the changes and the impacts on biodiversity. In general, impact assessments of hydroelectric power-plants on terrestrial invertebrates have been conducted after installation of the dam. Monitoring biodiversity is expensive, and shortcuts are often used to access this information. Therefore the use of the higher-taxon approach seems appropriate for this purpose. We investigated the effectiveness of ant genus-level at predicting ant species-level responses overtime in two grains of the spatial scale (site and plot) in the area of influence of a hydroelectric power-plant in the Amazon basin. We used a database from six sites, sampled over seven years in 14 ant collection events. The samplings were standardized, with five collection points along with 250 m plots. We tested whether the variation in the spatio-temporal scales affected the predictive power of genus-level for the metrics of richness and composition. We investigated if there is a difference in the predictive response of genera as surrogates for the species when using different spatial scales (site and plot) and also if the effectiveness of the prediction of genera changes over time. Also, we evaluated the effects of the species: genus ratio on the prediction of genera as a surrogate for species richness and composition.We recorded a high positive correlation between the richness of genera and species. Also, detected high congruence among the composition of genera and species, and no species:genus ratio effect in the evaluated spatio-temporal scales. Thus, the robustness of genus data to predict the species-level does not change over time at both spatial scales under the influence area of ​​a hydroelectric power-plant in the Amazon basin. It reinforces the use of the higher-taxon approach, which can be a useful and efficient tool in biodiversity studies or long-term monitoring.

Which Pitfall Traps and Sampling Effort to Choose to Evaluate Cropping System Effects on Spider and Carabid Assemblages?

In arable agroecosystems, arthropod communities often have a reduced abundance and diversity, which represents a challenge for sampling techniques needed to detect small differences among these simplified communities. We evaluated the suitability of pitfall traps for comparing the effects of cropping systems on arthropod communities. In a field experiment, we compared the effects of two pitfall trap diameters, the type of preserving fluid and the sampling effort on three metrics (activity density, taxonomic richness, and community weighted mean [CWM] of body size) for carabids and spiders. Trap size affected the observed composition of communities, with large traps yielding a higher proportion of spiders, and a higher richness and CWM body size for both taxa. The type of preserving fluid had a weaker effect. Simulations with various sampling efforts showed that only very different communities could be distinguished with less than 10 traps per field or less than 30 field replicates. Fewer traps were required to find differences between cropping systems for body size than for other metrics. Carabid activity density and body size, and spider genus richness, were the variables better distinguishing between cropping systems with the smallest sampling effort. A high sampling effort was required for comparing activity density and richness across cropping systems. Selection of the most appropriate trap design, metrics, and crops are the main factors for optimizing the trade-off between sampling effort and the ability to detect arthropod community responses to habitat management.

Abundance Tracking by Long-Read Nanopore Sequencing of Complex Microbial Communities in Samples from 20 Different Biogas/Wastewater Plants

Anaerobic digestion (AD) has long been critical technology for green energy, but the majority of the microorganisms involved are unknown and are currently not cultivable, which makes abundance tracking difficult. Developments in nanopore long-read sequencing make it a promising approach for monitoring microbial communities via metagenomic sequencing. For reliable monitoring of AD via long reads, we established a robust protocol for obtaining less fragmented, high-quality DNA, while preserving bacteria and archaea composition, for a broad range of different biogas reactors. Samples from 20 different biogas/wastewater reactors were investigated, and a median of 20.5 Gb sequencing data per nanopore flow cell was retrieved for each reactor using the developed DNA isolation protocol. The nanopore sequencing data were compared against Illumina sequencing data while using different taxonomic indices for read classifications. The Genome Taxonomy Database (GTDB) index allowed sufficient characterisation of the abundance of bacteria and archaea in biogas reactors with a dramatic improvement (1.8- to 13-fold increase) in taxonomic classification compared to the RefSeq index. Both technologies performed similarly in taxonomic read classification with a slight advantage for Illumina in regard to the total proportion of classified reads. However, nanopore sequencing data revealed a higher genus richness after classification. Metagenomic read classification via nanopore provides a promising approach to monitor the abundance of taxa present in a microbial AD community as an alternative to 16S ribosomal RNA studies or Illumina Sequencing.

Effects of mining and reduced turnover of Ephemeroptera (Insecta) in streams of the Eastern Brazilian Amazon

Mining operations can cause environmental alterations that have a major impact on aquatic organisms. In the present study, we analyzed the effects of mining operations on the environmental heterogeneity of streams in the eastern Brazilian Amazon, and the beta diversity (and components) of the local communities of the order Ephemeroptera. We tested three hypotheses: (a) mining activities reduce the environmental variation of streams; (b) altered streams have lower beta diversity, and (c) environmental variables influence the genus richness and abundance of ephemeropterans. The ephemeropterans were sampled in the Carajas National Forest in the dry season over 3 years. Streams were sampled in areas near the extraction of iron ore (16) and in pristine environments (8). The beta diversity was estimated based on the occurrence and abundance approaches. We recorded 2259 individuals and 32 genera. The comparative assessment of environmental variables indicated that environments altered by mining have higher total manganese and iron concentrations than preserved environments. Environmental variables influenced ephemeropteran communities, and the analysis of the components of the beta diversity indicated a higher turnover of ephemeropterans in preserved streams, which implies that species substitution rates are higher in preserved streams than in altered streams. These results indicate that the substitution of species in preserved streams is limited spatially, probably linked to the sensitivity of the organisms to oscillations in the environmental variables occurring in impacted environments. IMPLICATIONS FOR INSECT CONSERVATION: The results indicated that possibly the changes brought about by mining activities restrict the turnover of species between the preserved and altered areas, and only species tolerant to these changes were established. Over time and with the advancement of mining activities may occur the local exclusion of the most sensitive species and homogenization of the composition formed by more tolerant and less relevant conservation species.

Effects of sediment disturbance on deep-sea nematode communities: Results from an in-situ experiment at the arctic LTER observatory HAUSGARTEN

The present study examines the effects of experimentally generated disturbance on bathyal nematode communities at the LTER (Long-Term Ecological Research) observatory HAUSGARTEN, situated in the Fram Strait, between Greenland and Svalbard. In order to understand the complex interactions between the biota and environmental perturbations we deployed a free-falling device (bottom lander) equipped with three rotating fork-like disturber units, able to perturbate the upper sediment layers with different disturbance frequencies at chosen time intervals. During a one-year deployment at 2493 m water depth, disturber unit DI was programmed to rotate every 14 days, DII every 28 days, and DIII every 72 days, resulting in 28, 14, and 7 perturbations, respectively. Sediment sampling following this experimental period was conducted with push-coring devices deployed by the Remotely Operated Vehicle “QUEST 4000” (MARUM, Bremen). These sediment cores were sub-sampled to determine the effect of the sediment perturbations on various sediment parameters (i.e., grain size distribution, chloroplastic pigment concentrations) as well as on benthic nematode communities.A total of 4773 nematodes from 27 families and 81 genera were identified. Nematode densities in the disturbed areas ranged from 617 ind. / 10 cm2 to 1566 ind. / 10 cm2, with a mean density of 1193 ind. / 10 cm2 observed overall in the disturbed sediments. Control sediments contained on average 20% more nematode specimens than were found within the disturbed sediments, with an average density of 1477 ind. / 10 cm2 observed. Nematode evenness (J'), genera richness (EG(51)) and heterogeneity (H′) were not significantly different between the treatments and controls (undisturbed vs disturbance). We found a significant effect of the interaction of disturbance frequency and sediment depth (interaction term Fr x De) on heterogeneity and genera richness, while evenness significantly differed between different sediment depths (De) and within the disturbed sediments between different disturbance frequencies (Fr). Although surface sediments in the three disturbed areas were effectively perturbated, sediment depth still has the most pronounced influence on nematode community attributes, while the experimentally induced disturbance had only a limited impact on nematode diversity and community structure. Although we found the density of some nematode genera was negatively affected by the disturbances, the deep-sea nematode community at HAUSGARTEN was generally characterized by a relatively high diversity and seemed to be largely resilient to the experimental disturbances.

Comparing environmental DNA metabarcoding and underwater visual census to monitor tropical reef fishes

AbstractEnvironmental DNA (eDNA) analysis is a revolutionary method to monitor marine biodiversity from animal DNA traces. Examining the capacity of eDNA to provide accurate biodiversity measures in species‐rich ecosystems such as coral reefs is a prerequisite for their application in long‐term monitoring. Here, we surveyed two Colombian tropical marine reefs, the island of Providencia and Gayraca Bay near Santa Marta, using eDNA and underwater visual census (UVC) methods. We collected a large quantity of surface water (30 L per filter) above the reefs and applied a metabarcoding protocol using three different primer sets targeting the 12S mitochondrial DNA, which are specific to the vertebrates Actinopterygii and Elasmobranchii. By assigning eDNA sequences to species using a public reference database, we detected the presence of 107 and 85 fish species, 106 and 92 genera, and 73 and 57 families in Providencia and Gayraca Bay, respectively. Of the species identified using eDNA, 32.7% (Providencia) and 18.8% (Gayraca) were also found in the UVCs. We further found congruence in genus and species richness and abundance between eDNA and UVC approaches in Providencia but not in Gayraca Bay. Mismatches between eDNA and UVC had a phylogenetic and ecological signal, with eDNA detecting a broader phylogenetic diversity and more effectively detecting smaller species, pelagic species and those in deeper habitats. Altogether, eDNA can be used for fast and broad biodiversity surveys and is applicable to species‐rich ecosystems in the tropics, but improved coverage of the reference database is required before this new method could serve as an effective complement to traditional census methods.

Relationships between environmental variables and free-living nematode communities in seasonally flooded wetlands.

The Lo Go-Xa Mat is a national park in the southeastern region of Vietnam, which has a particularly high biodiversity and it includes different wetlands which are unique diverse in species composition. It can be categorized into two types: temporarily-seasonally and permanently flooded wetlands. Ta Not grassy marsh is representative of the seasonally flooded wetland. Whilst the diversity and ecology of plants and mammals are well documented, little or no information of the benthic ecology in the seasonally flooded wetland exist. This study aims to provide a new database of the nematode’s structure in the seasonally flooded wetland and its relation with environmental variables as well as detection of the ecological quality, considering nematodes as bioindicators. This work is the first investigation on nematodes communities in associate with some environmental variables in the Ta Not grassy marsh. The results showed that free-living nematodes in the Ta Not seasonally flooded grassy marsh are characterized by the high density (ranged from 235.01 to 898.43 inds.10cm-2) but rather low diversity. More specifically, the genus richness (S) ranged from 8.20 to 8.60. The observed Margalef’s species richness (d) was ranging from 1.07 to 1.53 and the Shannon-Wiener index (H') was measured from 2.36 to 2.52. In addition, the Pielou's evenness (J′) ranged from 0.55 to 0.68 and the Hill indices indicated average values ranging between 5.46- 5.84 for N1, between 4.32-4.60 for N2, and between 2.64-2.86 for Ninf. Specifically, our results indicated that deep level, pH, and NH4+ showed a significant correlation with the nematode density and bio-indices. The sediment of the Ta Not grassy marsh was assessed as in good conditions in all stations based on the Maturity Index of nematodes.

Divergent responses of nematodes in plant litter versus in top soil layer to nitrogen addition in a semi-arid grassland

Nematodes are a crucial component of the soil food web, and play a key role in maintaining biodiversity and regulating soil nutrient cycling. Many studies have been done on the effects of N addition on the soil biota, but the effects of N addition on nematodes in plant litter versus in soil are not well understood, especially in semi-arid steppe ecosystems. Here we investigated the composition of nematode communities in plant litter versus in surface soil in two climatically contrasting years in a simulated N enrichment experiment with four N levels (0, 25, 50 and 100 kg N ha−1 yr−1) in a temperate semi-arid grassland. We found that nematodes in plant litter were more sensitive to N addition than that in surface soil, that is, the abundance and generic richness of nematodes in plant litter, but not in surface soil, manifest a significant difference among N addition rates at both community and guild levels. The abundance and generic richness of nematodes were significantly higher in 2015 (a year with relatively wet weather) than 2016 (a year with relatively dry weather) in soil, but the opposite was true on the abundance of nematodes in litter. The plant parasites and omnivores-predators were more abundant, whereas the bacterivores and fungivores were less abundant, in 2015 than 2016. Our results also indicate that litter C/N ratio and soil moisture have greater impact than litter biomass and plant species richness on the abundance of nematodes in litter layer, while soil moisture and resource availability have greater impact than soil N availability and pH on the abundance of nematodes in the top soil. These results provide new insights into the dynamics of nematode communities, and suggest that the litter layer is very important to maintain a stable nematode community in the steppe ecosystem under the fluctuating climate.

The impact of planting buckwheat strips along lowbush blueberry fields on beneficial insects

Pollination and pest control are important in many agroecosystems. Beneficial insects that provide these services (e.g., bees and natural enemies) often require floral resources beyond crop bloom. Planting floral resources along crop field margins may be a useful tactic to support communities of beneficial insects in agroecosystems. We examined the effect of planting buckwheat (Fagopyrum esculentum Moench) along lowbush blueberry (Vaccinium angustifolium Aiton) field margins on beneficial insect abundance and generic richness. We found that bee abundance was higher in buckwheat transects than control transects in 2014 and 2015, but not 2016, and that bee generic richness was higher in buckwheat transects than in control transects in 2015 only. High variability occurred across years. All bee genera recorded during blueberry bloom were also collected in buckwheat transects, suggesting buckwheat is a useful resource for the bee community involved in blueberry pollination. The effect of buckwheat on natural enemies was variable and inconsistent. We conclude that buckwheat influenced bee and natural enemy communities during certain years, but field edges in the lowbush blueberry fields studied may already adequately support beneficial insects. Thus, not all habitat management efforts with augmentative floral plantings may consistently boost communities of beneficial insects.

Gastric Microbiome Diversities in Gastric Cancer Patients from Europe and Asia Mimic the Human Population Structure and Are Partly Driven by Microbiome Quantitative Trait Loci.

The human gastrointestinal tract harbors approximately 100 trillion microorganisms with different microbial compositions across geographic locations. In this work, we used RNASeq data from stomach samples of non-disease (164 individuals from European ancestry) and gastric cancer patients (137 from Europe and Asia) from public databases. Although these data were intended to characterize the human expression profiles, they allowed for a reliable inference of the microbiome composition, as confirmed from measures such as the genus coverage, richness and evenness. The microbiome diversity (weighted UniFrac distances) in gastric cancer mimics host diversity across the world, with European gastric microbiome profiles clustering together, distinct from Asian ones. Despite the confirmed loss of microbiome diversity from a healthy status to a cancer status, the structured profile was still recognized in the disease condition. In concordance with the parallel host-bacteria population structure, we found 16 human loci (non-synonymous variants) in the European-descendent cohorts that were significantly associated with specific genera abundance. These microbiome quantitative trait loci display heterogeneity between population groups, being mainly linked to the immune system or cellular features that may play a role in enabling microbe colonization and inflammation.