Alfa and beta diversity of thrips (Thysanoptera) and biological control agents in chrysanthemum flowers (Chrysanthemum sp.) of two ecoregions in Jujuy province, Argentina

The objectives of this study are to identify thrips and their biological controllers, to analyze their abundance in three flower opening stages stages of chrysanthemum crops, and to determine alpha and beta diversity in two ecoregions of Jujuy province (Argentina). The study was carried out in the Chaco ecoregion (ECH) in October and November 2016, and in the Prepuna ecoregion (EP) in February and March 2018. On each date, six replicates of five flowers were excised in the stages: flower bud , semi-open flower and open flower. Diversity profiles and rank-abundance curves were built, and Jaccard's coefficient of similarity was applied. The diversity profiles showed significant differences in thrips communities. In the ECH, 15 thrips species were identified; the dominant and permanent species were Microcephalothrips abdominalis (Crawford) and Frankliniella occidentalis (Pergande). Five species were recorded in the EP, although Frankliniella gemina Bagnall and Thrips tabaci Lindeman on their own represented 78% of the total abundance. In the ECH, 20 entomophagous species/morphospecies were recognized, and 19 in the EP; antocorids were dominant in both ecoregions. The thrips and the entomophagous communities of chrysanthemum flowers were different (34%) between the ecoregions studied.

Capture and Ex-Situ Analysis of Environmental Biofilms in Livestock Buildings

Little information about biofilm microbial communities on the surface of livestock buildings is available yet. While these spatially organized communities proliferate in close contact with animals and can harbor undesirable microorganisms, no standardized methods have been described to sample them non-destructively. We propose a reproducible coupon-based capture method associated with a set of complementary ex-situ analysis tools to describe the major features of those communities. To demonstrate the biofilm dynamics in a pig farm building, we analyzed the coupons on polymeric and metallic materials, as representative of these environments, over 4 weeks. Confocal laser scanning microscopy (CLSM) revealed a rapid coverage of the coupons with a thick layer of biological material and the existence of dispersed clusters of active metabolic microorganisms. After detaching the cells from the coupons, counts to quantify the CFU/cm2 were done with high reproducibility. High-throughput sequencing of the 16S rRNA V3-V4 region shows bacterial diversity profiles in accordance with reported bacteria diversity in pig intestinal ecosystems and reveals differences between materials. The coupon-based methodology allows us to deepen our knowledge on biofilm structure and composition on the surface of a pig farm and opens the door for application in different types of livestock buildings.

Spatial fungal community diversity profiles in pit mud samples from fermentation cellars used to manufacture Chinese Strong-flavour liquor

Background Few studies to date have sought to characterize the spatial profiles of pit mud microbial communities in fermentation cellars from Chinese strong-flavour liquor distilleries. This study was thus designed to evaluate these eukaryotic communities in pit mud samples via a multidimensional DGGE approach and by assessing associated sample physicochemical properties. Results Penicillium fuscoglaucum, Penicillium glandicola, Aotearoamyces nothofagi, Malassezia restricta, Penicillium lanosocoeruleum, Penicillium crustosum, and Aspergillus tonophilus were detected only in pit mud from the upper cellar wall, while Alternaria alstroemeriae, Trichosporon insectorum, Fusarium equiseti, Calonectria pseudoreteaudii, Penicillium clavigerum, Penicillium compactum, Ascochyta phacae, Metarhizium frigidum, Alternaria burnsii, Fusarium nurragi, and Didymella keratinophila were present only in the middle cellar wall layer. Alternaria zantedeschiae and Ilyonectria cyclaminicola were only present in pit mud samples from the lower cellar wall, while Leptobacillium leptobactrum, Calonectria queenslandica, Aspergillus appendiculatus, and Candida pseudolambica were only detected in pit mud from the cellar bottom. Moisture, pH, PO43−, acetic acid, humus, K+, Mg2+, Ca2+, acetic acid, butyric acid, and caproic acid levels in these different pit mud positions exhibited a rising incremental pattern from the upper wall layer to the bottom layer, whereas lactic acid levels were significantly lower in the bottom pit mud layer relative to other layers. Conclusions A clear relationship between fungal community structure and physicochemical variables in different spatial pit mud samples, especially moisture, pH, and NH4+-N were identified as the three most significant factors associated with fungal community through a redundancy analysis.

The Role of Small Lowland Patches of Exotic Forests as Refuges of Rare Endemic Azorean Arthropods

Islands have been disproportionately affected by the current biodiversity crisis. In island biotas, one of the most recurrent anthropic alterations is species introduction. Invasion of exotic species may represent a major threat for island biotas, because invasive species may change species composition and simplify community dynamics. We investigated diversity patterns of native and introduced species in native and exotic forests of Terceira Island (Azores, Portugal) by using diversity profiles based on Hill numbers. Use of diversity profiles allows for a complete characterization of the community diversity because they combine information on species richness, rarity, and dominance. We found that native forest remnants are crucial for the maintenance of endemic Azorean arthropod diversity. However, we also found that some lowland patches of exotic forests can sustain populations of rare endemic species. Our findings reinforce the importance of the few and small remnants of native forests, which are a pillar to the conservation of Azorean endemic arthropods. However, areas occupied by exotic forests, whether they are large and contiguous or small and isolated, close to native forests, or embedded in a matrix of agriculture activities, can also play a role in the conservation of native species, including endemics.

Adherence to Mediterranean diet impacts gastrointestinal microbial diversity throughout pregnancy

Background Consumption of a diet with high adherence to a Mediterranean diet pattern (MDP) has been associated with a favorable gastrointestinal tract (GIT) microbiome. A healthy GIT microbiome in pregnancy, as defined by increased alpha diversity, is associated with lower chance of adverse perinatal outcomes. This study aimed to evaluate the impact of adherence to an MDP on GIT microbial diversity longitudinally throughout pregnancy. Methods Adherence to MDP was scored by the Alternate Mediterranean (aMED) Diet Quality Score, after being applied to a validated Food Frequency Questionnaire. Association of aMED Scores with GIT alpha diversity profiles were compared linearly and across time using a linear mixed model, including covariates of age, body mass index (BMI), ethnicity, and parity. Results Forty-one participants of Filipino, Japanese, Native Hawaiian, and Non-Hispanic White descent provided dietary information and microbiome samples during each trimester of pregnancy. Alpha diversity profiles changed over gestation, with decreased microbial diversity in the third trimester. aMED scores positively correlated with Chao1 Index and Observed Species Number (r = 0.244, p = 0.017, and r = 0.233, p = 0.023, respectively). The strongest association was detected in the third trimester (Chao 1: r = 0.43, p = 0.020, Observed Species Number: r = 0.41, p = 0.026). Participants with higher aMED scores had higher relative abundance of Acidaminoacaeae at the family level (p = 0.0169), as well as higher abundance of several species known to increase production of short chain fatty acids within the GIT. Conclusions Adherence to MDP pattern is associated with increased maternal GIT microbial diversity, and promotes the abundance of bacteria that produce short chain fatty acids. Increased consumption of fruits, vegetables and legumes with low red meat consumption were key components driving this association. The effect of nutrition however, was less of an effect than pregnancy itself. Further studies are needed to determine if adherence to a Mediterranean diet translates not only into microbial health, but also into reduced risk of adverse pregnancy outcomes.

Signatures of genetic variation in human microRNAs point to processes of positive selection related to population-specific disease risks

The occurrence of natural variation in human microRNAs has been the focus of numerous studies during the last twenty years. Most of them have been dedicated to study the role of specific mutations in diseases, like cancer, while a minor fraction seek to analyse the diversity profiles of microRNAs in the genomes of human populations. In the present study we analyse the latest human microRNA annotations in the light of the most updated catalog of genetic variation provided by the 1000 Genomes Project. We show by means of the in silico analysis of noncoding variation of microRNAs that the level of evolutionary constraint of these sequences is governed by the interplay of different factors, like their evolutionary age or the genomic location where they emerged. The role of mutations in the shaping of microRNA-driven regulatory interactions is emphasized with the acknowledgement that, while the whole microRNA sequence is highly conserved, the seed region shows a pattern of higher genetic diversity that appears to be caused by the dramatic frequency shifts of a fraction of human microRNAs. We highlight the participation of these microRNAs in population-specific processes by identifying that not only the seed, but also the loop, are particularly differentiated regions among human populations. The quantitative computational comparison of signatures of population differentiation showed that candidate microRNAs with the largest differences are enriched in variants implicated in gene expression levels (eQTLs), selective sweeps and pathological processes. We explore the implication of these evolutionary-driven microRNAs and their SNPs in human diseases, such as different types of cancer, and discuss their role in population-specific disease risk.

Seasonal dynamics of waterbirds from a relict wetland in the central Monte Desert, Argentina

Wetlands currently have high rates of degradation, with more than 70% lost globally. In the central Monte Desert, Argentina, they are a scarce and limited resource for the biodiversity which depends on them. Waterbirds have been used as biological indicators of wetlands because they respond to fluctuations in food resources and to environmental changes in the short term. Here we analyse the seasonal variations in the structure of the waterbird assemblage from a relict wetland in this region. We carried out censuses of waterbirds in a 6-year period (between 2009 and 2019) during the southern summer and winter. We recorded 1875 individuals of 33 species of waterbirds during the summer and 677 individuals of 29 species during the winter. The grouping patterns of the waterbird assemblages differed between seasons (R = 0.35; p < 0.01). Taxonomic diversity profiles showed greater diversity for all indexes (qD) during the summer. The guild of invertivorous and omnivorous waders had a greater abundance of individuals during the summer (p < 0.05) and, together with the surface-feeding herbivores, contributed to the 87% of the dissimilarity of the assemblages between seasons. Phoenicopterus chilensis was the only species registered as threatened with national and international extinction. Relict wetlands, such as Laguna del Viborón, still have attributes of community diversity and represent the last refuges for waterbirds of the central Monte Desert. The information gathered in this study will contribute to the guidelines for integrated management plans and monitoring programmes for the conservation of the wetland and its biodiversity.

Invertebrates for vertebrate biodiversity monitoring: comparisons using three insect taxa as iDNA samplers

Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate-derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or feces. Here, we use metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) to profile gamma and alpha diversity in a dry, tropical forest in the southern Amazon. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. Carrion flies were the most effective sampler, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, in describing vertebrate biodiversity followed by sandflies. Camera traps had the highest median species richness at the site-level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host-vector interactions.

Invertebrates for vertebrate biodiversity monitoring: comparisons using three insect taxa as iDNA samplers

Metabarcoding of environmental DNA (eDNA) is now widely used to build diversity profiles from DNA that has been shed by species into the environment. There is substantial interest in the expansion of eDNA approaches for improved detection of terrestrial vertebrates using invertebrate-derived DNA (iDNA) in which hematophagous, sarcophagous, and coprophagous invertebrates sample vertebrate blood, carrion, or feces. Here, we use metabarcoding and multiple iDNA samplers (carrion flies, sandflies, and mosquitos) to profile gamma and alpha diversity in a dry, tropical forest in the southern Amazon. Our main objectives were to (1) compare diversity found with iDNA to camera trapping, which is the conventional method of vertebrate diversity surveillance and (2) compare each of the iDNA samplers to assess the effectiveness, efficiency, and potential biases associated with each sampler. Carrion flies were the most effective sampler, despite the least amount of sampling effort and the fewest number of individuals captured for metabarcoding, in describing vertebrate biodiversity followed by sandflies. Camera traps had the highest median species richness at the site-level but showed strong bias towards carnivore and ungulate species and missed much of the diversity described by iDNA methods. Mosquitos showed a strong feeding preference for humans as did sandflies for armadillos, thus presenting potential utility to further study related to host-vector interactions.

OTUs and ASVs Produce Comparable Taxonomic and Diversity from Shrimp Microbiota 16S Profiles Using Tailored Abundance Filters

The interplay between shrimp immune system, its environment, and microbiota contributes to the organism’s homeostasis and optimal production. The metagenomic composition is typically studied using 16S rDNA profiling by clustering amplicon sequences into operational taxonomic units (OTUs) and, more recently, amplicon sequence variants (ASVs). Establish the compatibility of the taxonomy, α, and β diversity described by both methods is necessary to compare past and future shrimp microbiota studies. Here, we used identical sequences to survey the V3 16S hypervariable-region using 97% and 99% OTUs and ASVs to assess the hepatopancreas and intestine microbiota of L. vannamei from two ponds under standardized rearing conditions. We found that applying filters to retain clusters >0.1% of the total abundance per sample enabled a consistent taxonomy comparison while preserving >94% of the total reads. The three sets turned comparable at the family level, whereas the 97% identity OTU set produced divergent genus and species profiles. Interestingly, the detection of organ and pond variations was robust to the clustering method’s choice, producing comparable α and β-diversity profiles. For comparisons on shrimp microbiota between past and future studies, we strongly recommend that ASVs be compared at the family level to 97% identity OTUs or use 99% identity OTUs, both using tailored frequency filters.