Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network

Distinct bacterial trophic networks exist in the gut microbiota of individuals in industrialized and non-industrialized countries. In particular, non-industrialized gut microbiomes tend to be enriched with Prevotella species. To study the development of these Prevotella-rich compositions, we investigated the gut microbiota of children aged between 7 and 37 months living in rural Gambia (616 children, 1,389 stool samples, stratified by 3-month age groups). These infants, who typically eat a high-fibre, low-protein diet, were part of a double-blind, randomized iron intervention trial (NCT02941081) and here we report the secondary outcome. We found that child age was the largest discriminating factor between samples and that anthropometric indices (collection time points, season, geographic collection site, and iron supplementation) did not significantly influence the gut microbiome. Prevotella copri, Faecalibacterium prausnitzii and Prevotella stercorea were, on average, the most abundant species in these 1,389 samples (35%, 11% and 7%, respectively). Distinct bacterial trophic network clusters were identified, centred around either P.stercorea or F.prausnitzii and were found to develop steadily with age, whereas P.copri, independently of other species, rapidly became dominant after weaning. This dataset, set within a critical gut microbial developmental time frame, provides insights into the development of Prevotella-rich gut microbiomes, which are typically understudied and are underrepresented in western populations.

Fishing triggers trophic cascade in terms of variation, not abundance in an allometric trophic network model

Trophic cascade studies often rely on linear food chains instead of complex food webs and are typically measured as biomass averages, not as biomass variation. We study trophic cascades propagating across a complex food web including a measure of biomass variation in addition to biomass average. We examined whether different fishing strategies induce trophic cascades and whether the cascades differ from each other. We utilized an allometric trophic network (ATN) model to mechanistically study fishing-induced changes in food-web dynamics. Different fishing strategies did not trigger traditional, reciprocal trophic cascades, as measured in biomass averages. Instead, fishing triggered a variation cascade that propagated across the food web including fish, zooplankton and phytoplankton species. In fisheries that removed a large amount of top-predatory and cannibalistic fish, the biomass oscillations started to decrease after fishing was started. In fisheries that mainly targeted large planktivorous fish, the biomass oscillations did not dampen, but slightly increased over time. Removing species with specific ecological functions might alter the food web dynamics and potentially affect the ecological resilience of aquatic ecosystems.

Multi-marker metabarcoding resolves subtle variations in freshwater condition: Bioindicators, ecological traits, and trophic interactions

Freshwater systems are experiencing rapid biodiversity losses resulting from high rates of habitat degradation. Ecological condition is typically determined through identifying either macroinvertebrate or diatom bioindicator assemblages and comparing them to their known tolerance to stressors. These comparisons are typically conducted at family or genus levels depending on the availability of taxonomic keys and expertise for focal groups. The objective of this study was to test whether a more taxonomically comprehensive assessment of communities in benthic samples can provide a different perspective of ecological conditions. DNA metabarcoding was used to identify macroinvertebrates and diatoms from kick-net samples collected from sites with different habitat status. Sites with good condition were associated with higher beta diversity as well as slightly higher directed connectance and modularity indicating higher resilience compared with fair condition sites. Indicator value and correlation analyses used DNA metabarcoding data to detect 29 site condition indicator species consistent with known bioindicators and expected relative tolerances. DNA metabarcoding and trophic network analysis also recovered 11 keystone taxa. This study demonstrates the importance of taxonomic breadth across trophic levels for generating biotic data to study ecosystem status, with the potential to scale-up ecological assessments of freshwater condition, trophic stability, and resilience.

Genomic adaptation of the picoeukaryote Pelagomonas calceolata to temperate iron-poor oceans revealed by a chromosome-scale genome sequence.

Eukaryotic phytoplankton are key actors in marine ecosystems, they contribute to atmospheric CO2 sequestration and supply organic matter to the trophic network. Among them, Pelagophytes (Stramenopiles) algae are a diverse class with coastal species causative of harmful algal blooms while others are cosmopolites and abundant in open ocean ecosystems. Despite their ecological importance, only a few genomic references exist limiting our capacity to identify them and study their adaptation mechanisms in a changing environment. Here, we report the complete chromosome-scale assembled genome sequence of Pelagomonas calceolata. We identified unusual large low-GC and gene-rich regions potentially hosting centromeres. These particular genomic structures could be explained by the absence of genes necessary for an important recombination pathway in this species. We identified a large repertoire of genes involved in inorganic nitrogen sensing and uptake as well as many genes replacing iron-required proteins potentially explaining its ecological success in oligotrophic waters. Finally, based on this high-quality assembly, we evaluated P. calceolata relative abundance in all oceans using environmental Tara datasets. Our results suggest that P. calceolata is one of the most abundant eukaryote species in the oceans with a relative abundance driven by the high temperature and iron-poor conditions. Collectively, these findings bring new insights into the biology and ecology of P. calceolata and lay the foundation for the analysis of the adaptation and acclimation strategy of this picophytoplankton.

Advances in understanding the biology and epidemiology of barley yellow dwarf virus (BYDV)

A tri-trophic network of domesticated grasses (host), various aphids (vector) and barley yellow dwarf virus (pathogen) species has been spread by humans from Eurasia to the rest of the world. Understanding how climate, natural and agricultural landscapes challenge pathogens, vectors, and their natural enemies and shape their dynamics is the key to managing this pathosystem. This chapter provides an overview of this complex system and its evolution. The chapter includes a case study of biological control of aphids causing wheat BYDV in Brazil. The current challenge is to create tools that integrate knowledge of this complex pathosystem and facilitate monitoring and decision making for rational management to reduce the burden of disease.

Microplastics in Nile tilapia (Oreochromis niloticus) from Lake Amatitlán

Microplastics are plastic particles smaller than 5 mm found in the environment, which can cause health problems for aquatic organisms and humans, being classified as emerging pollutants. In Guatemala, Lake Amatitlán is one of the most polluted lakes as it receives discharges of wastewater, treated and untreated, as well as other waste from Guatemala City and other major urban populations. In a recent study, microplastics were found in sediments in Lake Amatitlán, so it was necessary to determine whether the lake's fish are affected by these pollutants, which can be harmful to their health. This research aimed to determine the microplastics in fish from Lake Amatitlán, for which 65 specimens of Nile tilapia (Oreochromis niloticus) were collected in October and December 2020, and January 2021. The collected fish were dissected in the laboratory, where the number and type of microplastics were analyzed in the digestive tract, after their separation by digestion and filtration. Lines or fibers were the most common type of microplastics, found in 63 specimens (96.9% of the analyzed specimens), ranging from 0 to 27 lines/fibers per individual. The frequency of other types of microplastics found were 0-3 fragments/individual, 0-2 films/individual, and 0-4 foams/individual, while microspheres were not found in any specimen. The presence of microplastics in tilapia from Lake Amatitlán is an indicator of contamination in the lake by pollutants that could affect the trophic network and represents a risk for the fish consumers, requiring the attention of environmental and health authorities. Keywords: emerging pollutants, Guatemala, pollution.

Spatial distribution of sediment archaeal and bacterial communities relates to the source of organic matter and hypoxia – a biogeographical study on Lake Remoray (France)

Bottom waters hypoxia spreads in many lakes worldwide causing severe consequences on whole lakes trophic network. Here, we aimed at understanding the origin of organic matter stored in the sediment compartment and the related diversity of sediment microbial communities in a lake with deoxygenated deep water layers. We used a geostatistical approach to map and compare both the variation of organic matter and microbial communities in sediment. Spatialisation of C/N ratio and δ13C signature of sediment organic matter suggested that Lake Remoray was characterized by an algal overproduction which could be related to an excess of nutrient due to the close lake-watershed connectivity. Three spatial patterns were observed for sediment microbial communities after the hypoxic event, each characterized by specific genetic structure, microbial diversity and composition. The relative abundance variation of dominant microbial groups across Lake Remoray such as Cyanobacteria, Gammaproteobacteria, Deltaproteobacteria and Chloroflexi provided us important information on the lake areas where hypoxia occurs. The presence of methanogenic species in the deeper part of the lake suggests important methane production during hypoxia period. Taken together, our results provide an extensive picture of microbial communities' distribution related to quantity and quality of organic matter in a seasonally hypoxic lake.

RCaN: a software for Chance and Necessity modelling

Uncertainty is a challenge in modelling ecological systems and has been a source of misunderstandings between modelers and non-modelers. The "Chance and Necessity" (CaN) modelling approach has been proposed to address this issue, in the case of trophic network modelling. CaN modelling focuses exploring food-web trajectories that can satisfy fundamental physical and biological laws, while being compatible with observations and domain knowledge. This type of approach can facilitate discussion among actors as it promotes sharing of information and does not presuppose any knowledge of modelling practices. It is therefore suitable for participatory modelling , i.e. a modelling approach in which different actors can confront their knowledge and understanding of the marine system and of the associated uncertainties. One important ingredient to achieve participatory modelling is the availability of a modelling platform that is efficient, fast and transparent, so that all actors can understand and follow the modelling steps and choices, and can rapidly visualize and discuss the results. But, until now, there existed no software to easily perform CaN modelling. Here, we present RCaN and RCaNconstructor. Combined, these provide the first tool to build CaN models in an intuitive way that is 1) suitable within participatory frameworks, 2) transparent, 4) computationally efficient, 5) fully documented through the provision of meta-information and 6) supportive of exploratory analyses through predefined graphical functions.