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.

Trade-off between competition ability and invulnerability to predation in marine microbes; protist grazing versus viral lysis effects

Trade-offs between competition ability and invulnerability to predation are important mechanisms explaining how predation promotes bacterial diversity. However, existence of these trade-offs has apparently not been investigated in natural marine bacterial communities. Here, we address this question with growth-based measurements for each marine bacterial taxon by conducting on-board dilution experiments to manipulate predation pressure and using high-throughput sequencing to assess the response of bacterial communities. We determined that bacterial taxa with a higher predation-free growth rate were accompanied with higher predation-caused mortality, supporting existence of competitiveness-invulnerability trade-off. This trade-off was stronger and more consistent under viral lysis than protist grazing. In addition, predation generally flattened out the rank-abundance distribution and increased the evenness and richness of the bacterial community. These findings supported the 'Kill-the-Winner' hypothesis. All experiments supported a significant competitiveness-invulnerability trade-off, but there was substantial variation among bacterial communities in response to predation across experiments conducted in various sites and seasons. Therefore, we inferred that the Kill-the-Winner hypothesis is important but likely not the only deterministic mechanism explaining how predation shapes bacterial assemblages in natural marine systems.

Declining Abundance of Coccinellidae (Coleoptera) Among Crop and Prairie Habitats of Eastern South Dakota, USA

Lady (= ladybird) beetles (Coleoptera: Coccinellidae) provide agroecosystem services as major predators of aphids and other pests of field crops. Several native coccinellids in North America have declined in association with the introduction of invasive species of lady beetles. In particular, populations of three native species declined drastically (Coccinella transversoguttata richardsoni) or effectively disappeared (Coccinella novemnotata, Adalia bipunctata) from agricultural landscapes in eastern South Dakota, U.S.A., following establishment of an invasive coccinellid (Coccinella septempunctata) in the 1980s. Since then, two other non-native coccinellids (Harmonia axyridis and Hippodamia variegata) have established in eastern South Dakota, but long-term analysis of their impact on the aphidophagous coccinellid guild is lacking. This paper summarizes long-term results from 14 years (2007–2020) of sampling coccinellids by sweepnet and timed searches in five field crops and restored prairie in eastern South Dakota. In all, 17,338 aphidophagous coccinellids comprising 10 species were sampled. Two invasive species (Coc. septempunctata, Har. axyridis) were the third- and fourth-most abundant species, respectively. The seven most abundant species constituted 99% of all coccinellids sampled and were recorded from all six habitats. However, coccinellid species ranged considerably in their evenness of habitat use, resulting in differences in rank abundance among habitats. Coccinellid assemblages were similar for alfalfa and winter wheat, but not for other habitats, which possessed distinct coccinellid assemblages based on rank abundance. Annual abundance of coccinellids varied considerably within habitats, but declining trends were evident from significant negative regressions in annual abundance for adult and immature coccinellids in corn and adults in soybean. As a group, native adult coccinellids showed a significant declining trend in corn but not in other habitats, whereas trends for non-native adult coccinellids were non-significant in all habitats. Sample rates of coccinellids in alfalfa, spring grains, and corn in this study were 74, 26, and 6%, respectively, compared to that of a previous study from the region, further indicating substantial decreases in coccinellid abundance. Possible explanations and implications for observed patterns in coccinellid diversity and individual species abundances in field crops and restored prairie of eastern South Dakota are discussed with respect to prey, agronomic trends, and landscape factors.

Landscape Anthropization Affects Mosquito Diversity in a Deciduous Forest in Southeastern Mexico

Mosquitoes (Diptera: Culicidae) are considered the group of insects that most impacts human health. Land use change, conversion of conserved sites into agricultural environments, urbanization, defaunation, and introduction of domestic animals can affect mosquito diversity positively or negatively, increasing the risk of transmission of zoonotic diseases. Here, we describe the diversity of adult mosquitoes in two environments (deciduous forest and anthropized zone) over 2 yr (2014–2016), using eight CDC traps at each site in three climatic seasons (rainy, cold, and dry). We captured 795 individuals belonging to 22 species. We constructed rank-abundance curves to determine spatial and temporal changes in the mosquito communities. We measured alpha diversity using the Shannon index (H′), Shannon exponential (eH) and Simpson dominance (Ds), and beta diversity using Jaccard’s coefficient of similarity (Ij). The most abundant species were Culex quinquefasciatus (40.5%), Culex coronator (18.3%), and Anopheles pseudopunctipennis (12.4%). The highest mosquito diversity was in the deciduous forest during the rainy season. Beta diversity analysis showed that species overlap varied among climatic seasons, with the sites sharing 65% species during the rainy season, but only 33% of species during the dry season. We found differences in the diversity of mosquitoes at the two sites, and the mosquito assemblage of the anthropized zone was significantly different from that of the deciduous forest.

Characterizing the Uncultivated Microbial Minority: towards Understanding the Roles of the Rare Biosphere in Microbial Communities

Microbial communities are frequently numerically dominated by just a few species. Often, the long “tail” of the rank-abundance plots of microbial communities constitutes the so-called “rare biosphere,” microorganisms that are highly diverse but are typically found in low abundance in these communities.

Phylogeny- and Abundance-Based Metrics Allow for the Consistent Comparison of Core Gut Microbiome Diversity Indices Across Host Species

The filtering of gut microbial datasets to retain high prevalence taxa is often performed to identify a common core gut microbiome that may be important for host biological functions. However, prevalence thresholds used to identify a common core are highly variable, and it remains unclear how they affect diversity estimates and whether insights stemming from core microbiomes are comparable across studies. We hypothesized that if macroecological patterns in gut microbiome prevalence and abundance are similar across host species, then we would expect that increasing prevalence thresholds would yield similar changes to alpha diversity and beta dissimilarity scores across host species datasets. We analyzed eight gut microbiome datasets based on 16S rRNA gene amplicon sequencing and collected from different host species to (1) compare macroecological patterns across datasets, including amplicon sequence variant (ASV) detection rate with sequencing depth and sample size, occupancy-abundance curves, and rank-abundance curves; (2) test whether increasing prevalence thresholds generate universal or host-species specific effects on alpha and beta diversity scores; and (3) test whether diversity scores from prevalence-filtered core communities correlate with unfiltered data. We found that gut microbiomes collected from diverse hosts demonstrated similar ASV detection rates with sequencing depth, yet required different sample sizes to sufficiently capture rare ASVs across the host population. This suggests that sample size rather than sequencing depth tends to limit the ability of studies to detect rare ASVs across the host population. Despite differences in the distribution and detection of rare ASVs, microbiomes exhibited similar occupancy-abundance and rank-abundance curves. Consequently, increasing prevalence thresholds generated remarkably similar trends in standardized alpha diversity and beta dissimilarity across species datasets until high thresholds above 70%. At this point, diversity scores tended to become unpredictable for some diversity measures. Moreover, high prevalence thresholds tended to generate diversity scores that correlated poorly with the original unfiltered data. Overall, we recommend that high prevalence thresholds over 70% are avoided, and promote the use of diversity measures that account for phylogeny and abundance (Balance-weighted phylogenetic diversity and Weighted Unifrac for alpha and beta diversity, respectively), because we show that these measures are insensitive to prevalence filtering and therefore allow for the consistent comparison of core gut microbiomes across studies without the need for prevalence filtering.

Diversity patterns of Middle Permian gastropod assemblages from the Tak Fa Formation, Central Thailand

Middle Permian marine invertebrate assemblages from Central Thailand are strongly dominated by gastropods. Two gastropod assemblages from the Tak Fa Limestone at Khao Noi and Khao Chao Thong of the Nakhon Sawan area are the first Permian ones from Thailand that are analysed regarding diversity and composition based on quantitative data. Both gastropod assemblages, comprising 40 species in total, are dominated by the gastropods Anomphalus sp., Warthia cf. brevisinuata and Glabrocingulum magnum; the genus Anomphalus is especially abundant which is unusual for Permian assemblages. Both studied gastropod assemblages have a similar taxonomic composition and diversity including the same values of diversity indices that indicate a moderate diversity. In addition, rarefaction analyses and rank-abundance distributions also suggest that diversity and structure of both assemblages are the same. The studied assemblage is compared with other Permian gastropod assemblages from Asia (Malaysia, East Timor and Japan). Rarefaction, diversity indices and rank-abundance distributions suggest that the diversity of the studied fauna is distinctly lower than that of the others despite coming from similar depositional environments. This is surprising because the Tak Fa gastropods lived at lower latitudes than the others. This could suggest an inverse diversity gradient in the Palaeo-Tethys, but more evidence is needed to substantiate this assumption. Several Late Palaeozoic and Early Mesozoic fossil assemblages are dominated by gastropods, e.g. those from the Pennsylvanian Buckhorn Asphalt deposit, the Permian from Japan and Malaysia, as well as the Late Triassic Cassian Formation. This shows that at least locally, gastropod dominance is not restricted to modern faunas.

Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros

Concerted evolution is a process of homogenisation of repetitive sequences within a genome through unequal crossing over and gene conversion. This homogenisation is never fully achieved because mutations always create new variants. Classically, concerted evolution has been detected as “noise” in electropherograms and these variants have been characterised through cloning and sequencing of subsamples of amplified products. However, this approach limits the number of detectable variants and provides no information about the abundance of each variant. In this study, we investigated concerted evolution by using environmental time-series metabarcoding data, single strain high-throughput sequencing (HTS) and a collection of Sanger reference barcode sequences. We used six species of the marine planktonic diatom genus Chaetoceros as study system. Abundance plots obtained from environmental metabarcoding and single strain HTS showed the presence of a haplotype far more abundant than all the others (the “dominant” haplotype) and identical to the reference sequences of that species obtained with Sanger sequencing. This distribution fitted best with Zipf’s law among the rank abundance/ dominance models tested. Furthermore, in each strain 99% of reads showed a similarity of 99% with the dominant haplotype, confirming the efficiency of the homogenisation mechanism of concerted evolution. We also demonstrated that minor haplotypes found in the environmental samples are not only technical artefacts, but mostly intragenomic variation generated by incomplete homogenisation. Finally, we showed that concerted evolution can be visualised inferring phylogenetic networks from environmental data. In conclusion, our study provides an important contribution to the understanding of concerted evolution and to the interpretation of DNA barcoding and metabarcoding data based on multigene family markers.

Microbial Community Analysis Using MiSeq Sequencing and Pathway of Methane Production in Tehran WWTP: A Full-Scale Anaerobic Digester

Introduction: One of biological wastewater treatment methods that utilizes to both digesting waste activated sludge and methane production is anaerobic digestion (AD). It is believed to be most effective solution in terms of energy crisis and environmental pollution issues. Materials and Methods: In this study the sludge was digested anaerobically sampled from a full-scale WWTP, located at south of Tehran, Iran for evaluation. To study the microbial community within the sludge the MiSeq Sequencing method utilized. Based on our field data (data not shown) and microbial community data, a schematic diagram of probable leading pathways was made in the studied digester. Results: At first, the community variety in the bulk sludge and richness were enhanced followed by loading increasing. Meanwhile, the loading change enhanced the community richness and variety of the sludge. By comparing the rank-abundance distributions, a shallow gradient would show high evenness since the abundances of diverse species are alike. The results showed all the communities were extremely diverse and 15 phyla were distinguished in the sludge sample. The dominant phyla of the community were Bacteroidetes and Firmicutes and quantity of the two phyla were 21% and 11%, respectively. Anaerobaculum, Acinetobacter, Syntrophomonas, and Coprothermobacter were the chief genera for the microbial communities and the sum of four genera were 7%, 3%, 3%, and 2%, respectively. Conclusion: It was shown that syntrophic acetate oxidizing bacterias (SAOBs) metabolized acetate through hydrogen trophic methanogenesis in the digester. Generally, the findings may be useful to help the wastewater operators to utilize an effective method that able to treat waste sludge plus methane production, simultaneously.