Reinvestigating the phylogeny of Myriapoda with more extensive taxon sampling and novel genetic perspective

Background There have been extensive debates on the interrelationships among the four major classes of Myriapoda—Chilopoda, Symphyla, Diplopoda, and Pauropoda. The core controversy is the position of Pauropoda; that is, whether it should be grouped with Symphyla or Diplopoda as a sister group. Two recent phylogenomic studies separately investigated transcriptomic data from 14 and 29 Myriapoda species covering all four groups along with outgroups, and proposed two different topologies of phylogenetic relationships. Methods Building on these studies, we extended the taxon sampling by investigating 39 myriapods and integrating the previously available data with three new transcriptomic datasets generated in this study. Our analyses present the phylogenetic relationships among the four major classes of Myriapoda with a more abundant taxon sampling and provide a new perspective to investigate the above-mentioned question, where visual genes’ identification were conducted. We compared the appearance pattern of genes, grouping them according to their classes and the visual pathways involved. Positive selection was detected for all identified visual genes between every pair of 39 myriapods, and 14 genes showed positive selection among 27 pairs. Results From the results of phylogenomic analyses, we propose that Symphyla is a sister group of Pauropoda. This stance has also received strong support from tree inference and topology tests.

Benthic molluscs collected in Western Antarctica during the “Caldas”, “Admiral Padilla” and “Admiral Campos” expeditions, southern summers 2014-2015, 2016-2017 and 2018-2019

This research is part of the results of the three first expeditions of Colombia to West Antarctica and it focused on the systematics and taxonomic diversity of the benthic community of molluscs collected between 5 and 400 m deep. The Sampling sites where mollusks were collected were located along the Gerlache and Bransfield straits, around the Palmer Archipelago and the South Shetland Islands, adjacent to the Antarctic Peninsula. The list of identified species that are deposited in the Museum of Marine Natural History of Colombia - Makuriwa, of the Institute of Marine and Coastal Research “José Benito Vives de Andréis” -Invemar, is presented. This inventory consisted of 15 specimens distributed in 10 taxa, of which 7 were shelled gastropods (including 5 microgastropods) and 3 were bivalves. Four microgastropods were placed in greater taxonomic categories due to the low knowledge of these taxa in the region (Anatoma sp., Cingulopsoidea sp., Truncatelloidea sp. and Eatoniella sp.). The other gastropod species (3) were Margarella antarctica, Prosipho turritus and Nacella concinna. The bivalves found were Philobrya sublaevis, Adacnarca nitens and Thracia meridionalis. The identified species have previously been recorded in West Antarctica. Some of them, like the bivalves, show a circumantarctic distribution. Nacella concinna was the most abundant taxon. In coherence with the general objective of the “BioGerlache-Antarctica” project, the results generate contributions to the biological inventories of Antarctica, contributing to expand the information to define possible conservation areas in the future.

Multiple integrated metabolic strategies allow foraminiferan protists to thrive in anoxic marine sediments

Oceanic deoxygenation is increasingly affecting marine ecosystems; many taxa will be severely challenged, yet certain nominally aerobic foraminifera (rhizarian protists) thrive in oxygen-depleted to anoxic, sometimes sulfidic, sediments uninhabitable to most eukaryotes. Gene expression analyses of foraminifera common to severely hypoxic or anoxic sediments identified metabolic strategies used by this abundant taxon. In field-collected and laboratory-incubated samples, foraminifera expressed denitrification genes regardless of oxygen regime with a putative nitric oxide dismutase, a characteristic enzyme of oxygenic denitrification. A pyruvate:ferredoxin oxidoreductase was highly expressed, indicating the capability for anaerobic energy generation during exposure to hypoxia and anoxia. Near-complete expression of a diatom’s plastid genome in one foraminiferal species suggests kleptoplasty or sequestration of functional plastids, conferring a metabolic advantage despite the host living far below the euphotic zone. Through a unique integration of functions largely unrecognized among “typical” eukaryotes, benthic foraminifera represent winning microeukaryotes in the face of ongoing oceanic deoxygenation.

Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron

Bacteroides is a highly abundant taxon in the human gut, and Bacteroides thetaiotaomicron (B. theta) is a ubiquitous human symbiont that colonizes the host early in development and persists throughout its life span. The phenotypic plasticity of keystone organisms such as B. theta is important to understand in order to predict phenotype(s) and metabolic interactions under changing nutrient conditions such as those that occur in complex gut communities. Our study shows B. theta prioritizes energy conservation and suppresses secretion of “overflow metabolites” such as organic acids and amino acids when concentrations of acetate are high. Secreted metabolites, especially amino acids, can be a source of nutrients or signals for the host or other microbes in the community. Our study suggests that when metabolically stressed by acetate, B. theta stops sharing with its ecological partners.

Metabarcoding Analysis of the Bacterial and Fungal Communities during the Maturation of Preparation 500, Used in Biodynamic Agriculture, Suggests a Rational Link between Horn and Manure

Horn manure (Preparation 500) is a product used in the practice of biodynamic agriculture. It is obtained by an underground fermentation of cow faecal material incubated in cow horns for several months. The product is used as spray treatment meant to increase soil fertility. In the present report we analyzed the successional changes in bacterial and fungal communities throughout the process of horn manure maturation by high throughput sequencing of ribosomal 16S (bacterial) and ITS (fungal) gene markers. Marked shifts in the microbial community were seen involving a general decrease from a Firmicutes-dominated material to a product transiently enriched in Proteobacteria and later in Actinobacteria, mostly within the Nocardioidaceae family. In the fungal community evolution, the most abundant taxon in the starting faecal material resulted a member of the Onygenales order, known to specifically degrade keratin. Its abundance in the intestine is explained by the fact that keratin, which is also the structural component of hairs and horns, is found in all epithelial layers, including gut mucosae. This occurrence suggests a link of enzymatic/catabolic nature between manure and horn.

Systematics and distribution of decapod crustaceans associated with late Eocene coral buildups from the southern Pyrenees (Spain)

A new decapod crustacean assemblage associated with late Eocene coral reef deposits in northeast Spain (southern Pyrenees) is recorded; it includes Gemmellarocarcinus riglosensis sp. nov., Daira corallina sp. nov., Lobogalenopsis joei sp. nov., Liopsalis cf. anodon (Bittner, 1875) and Galenopsis crassifrons A. Milne- Edwards, 1865. The genera Gemmellarocarcinus, Daira and Lobogalenopsis are here recorded for the first time from Eocene strata of the Iberian Peninsula, extending their palaeobiogeographical distribution. Detailed sampling from three different coral reef facies within the La Peña buildup, here referred to as branching, tabular and massive, suggest that the core of the reef, which was dominated by branching corals, hosted the highest diversity and abundance of decapod crustaceans. Daira corallina sp. nov. predominated in the branching corals facies, while G. crassiforns was the most abundant taxon within the tabular coral facies and carpiliids showed preferences for environments with massive corals. Thus, this constitutes a good example of primary ecological zonation among decapod crustaceans within a discrete reef.

Cross-Feeding between Members of Thauera spp. and Rhodococcus spp. Drives Quinoline-Denitrifying Degradation in a Hypoxic Bioreactor

ABSTRACT The complex bacterial community in a quinoline-degrading denitrifying bioreactor is predominated by several taxa, such as Thauera and Rhodococcus. However, it remains unclear how the interactions between the different bacteria mediate quinoline metabolism under denitrifying conditions. In this study, we designed a sequence-specific amplification strategy to isolate the most predominant bacteria and obtained four strains of Thauera aminoaromatica, a representative of a key member in the bioreactor. Tests on these isolates demonstrated that all were unable to degrade quinoline but efficiently degraded 2-hydroxyquinoline, the hypothesized primary intermediate of quinoline catabolism, under nitrate-reducing conditions. However, another isolate, Rhodococcus sp. YF3, corresponding to the second most abundant taxon in the same bioreactor, was found to degrade quinoline via 2-hydroxyquinoline. The end products and removal rate of quinoline by isolate YF3 largely varied according to the quantity of available oxygen. Specifically, quinoline could be converted only to 2-hydroxyquinoline without further transformation under insufficient oxygen conditions, e.g., less than 0.5% initial oxygen in the vials. However, resting YF3 cells aerobically precultured in medium with quinoline could anaerobically convert quinoline to 2-hydroxyquinoline. A two-strain consortium constructed with isolates from Thauera (R2) and Rhodococcus (YF3) demonstrated efficient denitrifying degradation of quinoline. Thus, we experimentally verified that the metabolic interaction based on 2-hydroxyquinoline cross-feeding between two predominant bacteria constitutes the main quinoline degradation mechanism. This work uncovers the mechanism of quinoline removal by two cooperative bacterial species existing in denitrifying bioreactors. IMPORTANCE We experimentally verified that the second most abundant taxon, Rhodococcus, played a role in degrading quinoline to 2-hydroxyquinoline, while the most abundant taxon, Thauera, degraded 2-hydroxyquinoline. Metabolites from Thauera further served to provide metabolites for Rhodococcus. Hence, an ecological guild composed of two isolates was assembled, revealing the different roles that keystone organisms play in the microbial community. This report, to the best of our knowledge, is the first on cross-feeding between the initial quinoline degrader and a second bacterium. Specifically, the quinoline degrader (Rhodococcus) did not benefit metabolically from quinoline degradation to 2-hydroxyquinoline but instead benefited from the metabolites produced by the second bacterium (Thauera) when Thauera degraded the 2-hydroxyquinoline. These results could be a significant step forward in the elucidation of the microbial mechanism underlying quinoline-denitrifying degradation.

Cross-feeding between Thauera aminoaromatica and Rhodococcus pyridinivorans drove quinoline biodegradation in a denitrifying bioreactor

The complex bacterial community is predominated by several taxa, such as Thauera and Rhodococcus, in a quinoline-degrading denitrifying bioreactor. Yet it remains unclear about how the interactions between the different bacteria mediate the quinoline metabolism in denitrifying condition. In this study, we designed a sequence-specific amplification to guide the isolation of the most predominant bacteria and obtained four strains of Thauera aminoaromatica, the representative of one key member in the bioreactor. Test on these isolates demonstrated that all of them were unable to strive on quinoline but could efficiently degrade 2-hydroxyquinoline, the hypothesized primary intermediate of quinoline catabolism, under nitrate-reducing condition. However, another isolate, Rhodococcus pyridinivorans YF3, corresponding to the second abundant taxon in the same bioreactor, was found to degrade quinoline via 2-hydroxyquinoline. The end products and removal rate of quinoline by isolate YF3 were largely varied with the quantity of available oxygen. Specifically, quinoline could only be converted into 2-hydroxyquinoline without further transformation under the condition with insufficient oxygen, e.g. less than 0.5% initial oxygen in the vials. However, if were aerobically pre-cultured in the medium with quinoline the resting cells of YF3 could anaerobically convert quinoline into 2-hydroxyquinoline. A two-strain consortium constructed with isolates from Thauera (R2) and Rhodococcus (YF3) demonstrated an efficient denitrifying degradation of quinoline. Thus, we experimentally proved that the metabolism interaction based on the 2-hydroxyquinoline cross-feeding between two predominant bacteria constituted the mainstream of quinoline degradation. This work sheds light on the understanding of mechanism of quinoline removal in the denitrifying bioreactor.ImportanceWe experimentally verified the most predominant Thauera sp. was indeed active degrader for the intermediate metabolites and the second abundant taxon Rhodococcus exerted, however, key function for opening the food box for a complex quinoline-degrading community. An ecological guild composed of two isolates was assembled, revealing the different roles of keystone organisms in the microbial community. This study, to our best knowledge, is the first report on the cross feeding between the initial attacker with unprofitable catalysis of reluctant heterocyclic compounds and the second bacterium which then completely degrade the compound transformed by the first bacterium. These results could be a significant step forward towards elucidation of microbial mechanism for quinoline denitrifying degradation.

Composition and diversity of benthic macroinvertebrates in a Brazilian Cerrado stream

ABSTRACT This study aimed to analyse the diversity and composition of benthic macroinvertebrate assemblages in the dry and rainy seasons in a Brazilian Cerrado stream, where it was hypothesized that the dry season has higher diversity and it differs in terms of organism composition in relation to the rainy season. Sampling was carried out in the dry (May and August/2016 and August/2017) and rainy seasons (November/2016 and February and November/2017). Individuals were identified at the family level and classified according to functional feeding group (FFG). There were 3,776 individuals, in which Chironomidae was the most abundant taxon with 2,226 organisms. The FFG with the highest number of individuals and species richness were collector-gatherer and predator, respectively. The species richness was higher in the dry season than in the rainy season. The ordinance generated by NMDS showed that there was no distinction in the composition of the assemblage between the dry and rainy seasons. Seasonal variations do not alter the abundance and composition of the benthic macroinvertebrate assemblage, but the species richness does decrease in rainy seasons.

Spatial variation of meiofaunal tardigrades in a small tropical estuary (~6°S; Brazil)

Spatial variations and organism–sediment relationship are paramount subjects of soft-bottom ecology. However, these issues have been unexplored for most minor meiofaunal taxa such as tardigrades. In the present study, we explore this subject on a small tropical (~6°S) estuary. Total meiofaunal abundance ranged from 4 to 1036 individuals per 10cm2, averaging (mean±s.d.) 324.8±245.9 individuals per 10cm2. Nematodes dominated in both seasons, representing >70% of total abundance. Tardigrades were the second-most abundant taxon, representing 15% of the total and up to 71%. Tardigrades were represented by two species, Batillipes dandarae and B. pennaki, the latter dominating in the rainy season, and both with similar abundances in the dry season. Abundance of total meiofauna and both tardigrade species differed significantly (ANOVA; P<0.05) among stations and in the interaction between stations and seasons, but only B. dandarae varied seasonally, with higher values occurring in the dry season. The spatial variations observed were mostly related to differences in the sediment granulometry. Environmental explanatory variables explained 72.6% of the variance of dominant meiofaunal taxa in the Redundancy Analysis. Nematodes and ostracods were mostly associated with fine and very fine sands, both tardigrades with medium sand and oligochaetes with larger size-fractions of the sediment and organic matter. The data gathered here suggest that granulometry was the most important environmental factor in the meiofaunal spatial structure in tropical estuaries and both tardigrade species were closely associated with medium sand.