Contribution of neutral processes to the assembly of gut microbial communities in the zebrafish over host development

Despite their importance to host health and development, the communities of microorganisms associated with humans and other animals are characterized by a large degree of unexplained variation across individual hosts. The processes that drive such inter-individual variation are not well understood. To address this, we surveyed the microbial communities associated with the intestine of the zebrafish, Danio rerio, over developmental time. We compared our observations of community composition and distribution across hosts with that predicted by a neutral assembly model, which assumes that community assembly is driven solely by chance and dispersal. We found that as hosts develop from larvae to adults, the fit of the model to observed microbial distributions decreases, suggesting that the relative importance of non-neutral processes, such as microbe-microbe interactions, active dispersal, or selection by the host, increases as hosts mature. We also observed that taxa which depart in their distributions from the neutral prediction form ecologically distinct sub-groups, which are phylogenetically clustered with respect to the full metacommunity. These results demonstrate that neutral processes are sufficient to generate substantial variation in microbiota composition across individual hosts, and suggest that potentially unique or important taxa may be identified by their divergence from neutral distributions

The composition of the zebrafish intestinal microbial community varies across development

The assembly of resident microbial communities is an important event in animal development; however, the extent to which this process mirrors the developmental programs of host tissues is unknown. Here we surveyed the intestinal bacteria at key developmental time points in a sibling group of 135 individuals of a model vertebrate, the zebrafish (Danio rerio). Our survey revealed stage-specific signatures in the intestinal microbiota and extensive interindividual variation, even within the same developmental stage. Microbial community shifts were apparent during periods of constant diet and environmental conditions, as well as in concert with dietary and environmental change. Interindividual variation in the intestinal microbiota increased with age, as did the difference between the intestinal microbiota and microbes in the surrounding environment. Our results indicate that zebrafish intestinal microbiota assemble into distinct communities throughout development, and that these communities are increasingly different from the surrounding environment and from one another

Local domestication of lactic acid bacteria via cassava beer fermentation

Cassava beer, or chicha, is typically consumed daily by the indigenous Shuar people of the Ecuadorian Amazon. This traditional beverage made from cassava tuber (Manihot esculenta) is thought to improve nutritional quality and flavor while extending shelf life in a tropical climate. Bacteria responsible for chicha fermentation could be a source of microbes for the human microbiome, but little is known regarding the microbiology of chicha. We investigated bacterial community composition of chicha batches using Illumina high-throughput sequencing. Fermented chicha samples were collected from seven Shuar households in two neighboring villages in the Morona-Santiago region of Ecuador, and the composition of the bacterial communities within each chicha sample was determined by sequencing a region of the 16S ribosomal gene. Members of the genus Lactobacillus dominated all samples. Significantly greater phylogenetic similarity was observed among chicha samples taken within a village than those from different villages. Community composition varied among chicha samples, even those separated by short geographic distances, suggesting that ecological and/or evolutionary processes, including human-mediated factors, may be responsible for creating locally distinct ferments. Our results add to evidence from other fermentation systems suggesting that traditional fermentation may be a form of domestication, providing endemic beneficial inocula for consumers, but additional research is needed to identify the mechanisms and extent of microbial dispersal

Ontogenetic Differences in Dietary Fat Influence Microbiota Assembly in the Zebrafish Gut

ABSTRACT Gut microbiota influence the development and physiology of their animal hosts, and these effects are determined in part by the composition of these microbial communities. Gut microbiota composition can be affected by introduction of microbes from the environment, changes in the gut habitat during development, and acute dietary alterations. However, little is known about the relationship between gut and environmental microbiotas or about how host development and dietary differences during development impact the assembly of gut microbiota. We sought to explore these relationships using zebrafish, an ideal model because they are constantly immersed in a defined environment and can be fed the same diet for their entire lives. We conducted a cross-sectional study in zebrafish raised on a high-fat, control, or low-fat diet and used bacterial 16S rRNA gene sequencing to survey microbial communities in the gut and external environment at different developmental ages. Gut and environmental microbiota compositions rapidly diverged following the initiation of feeding and became increasingly different as zebrafish grew under conditions of a constant diet. Different dietary fat levels were associated with distinct gut microbiota compositions at different ages. In addition to alterations in individual bacterial taxa, we identified putative assemblages of bacterial lineages that covaried in abundance as a function of age, diet, and location. These results reveal dynamic relationships between dietary fat levels and the microbial communities residing in the intestine and the surrounding environment during ontogenesis. IMPORTANCE The ability of gut microbiota to influence host health is determined in part by their composition. However, little is known about the relationship between gut and environmental microbiotas or about how ontogenetic differences in dietary fat impact gut microbiota composition. We addressed these gaps in knowledge using zebrafish, an ideal model organism because their environment can be thoroughly sampled and they can be fed the same diet for their entire lives. We found that microbial communities in the gut changed as zebrafish aged under conditions of a constant diet and became increasingly different from microbial communities in their surrounding environment. Further, we observed that the amount of fat in the diet had distinct age-specific effects on gut community assembly. These results reveal the complex relationships between microbial communities residing in the intestine and those in the surrounding environment and show that these relationships are shaped by dietary fat throughout the life of animal hosts

The Role of Microbial Communities in Tropical Ecosystems

Tropical ecosystems are different in important ways from those of temperate regions. They are a major reservoir of plant and animal biodiversity and play important roles in global climate regulation and biogeochemical cycling. They are also under great threat due to the conversion of tropical ecosystems to other uses. Thus, in the context of global change, it is crucial to understand how environmental factors, biogeographic patterns, and land use changes interact to influence the structure and function of microbial communities in these ecosystems. The contributions to this Research Topic showcase the current knowledge regarding microbial ecology in tropical ecosystems, identify many challenges and questions that remain to be addressed and open up new horizons in our understanding of the environmental and anthropological factors controlling microbial communities in these important ecosystems.Tropical ecosystems are different in important ways from those of temperate regions. They are a major reservoir of plant and animal biodiversity and play important roles in global climate regulation and biogeochemical cycling. They are also under great threat due to the conversion of tropical ecosystems to other uses. Thus, in the context of global change, it is crucial to understand how environmental factors, biogeographic patterns, and land use changes interact to influence the structure and function of microbial communities in these ecosystems. The contributions to this Research Topic showcase the current knowledge regarding microbial ecology in tropical ecosystems, identify many challenges and questions that remain to be addressed and open up new horizons in our understanding of the environmental and anthropological factors controlling microbial communities in these important ecosystems

Land-use change drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in Rondônia, Brazil

The Amazon Rainforest plays major roles in global carbon and nitrogen cycling. Despite this region’s immense importance, deforestation and pasture creation are still occurring at alarming rates. In this study, we investigated the effects of land-use change on aerobic ammonia-oxidizers in primary rainforest, young and old pasture, and secondary forest in Rondônia, Brazil. Forest-to-pasture conversion decreased soil nitrate, phosphorus, and exchangeable acidity contents that recovered to pre-disturbance levels as pastures aged or were abandoned and formed secondary forest. The ammonia-oxidizing community, numerically dominated by thaumarchaea, shifted due to land-use change, both in terms of gene abundance and community structure. However, thaumarchaeal ammonia monooxygenase gene abundances did not correlate with any measured soil physicochemial parameters. Phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, the nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal genus, the Nitrosotalea, indicates that land-use change can have long lasting effects on large portions of the thaumarchaeal community. The results of this study can be used as a conceptual foundation for determining how ammonia-oxidizers become altered by land-use change in South American tropical forests

Land-use change drives abundance and community structure alterations of thaumarchaeal ammonia oxidizers in tropical rainforest soils in Rondônia, Brazil

The Amazon Rainforest plays major roles in global carbon and nitrogen cycling. Despite this region’s immense importance, deforestation and pasture creation are still occurring at alarming rates. In this study, we investigated the effects of land-use change on aerobic ammonia-oxidizers in primary rainforest, young and old pasture, and secondary forest in Rondônia, Brazil. Forest-to-pasture conversion decreased soil nitrate, phosphorus, and exchangeable acidity contents that recovered to pre-disturbance levels as pastures aged or were abandoned and formed secondary forest. The ammonia-oxidizing community, numerically dominated by thaumarchaea, shifted due to land-use change, both in terms of gene abundance and community structure. However, thaumarchaeal ammonia monooxygenase gene abundances did not correlate with any measured soil physicochemial parameters. Phylogenetic analyses showed that community structural changes in ammonia-oxidizing thaumarchaea are driven by a shift away from primary rainforest, old pasture, and secondary forest clusters to separate clusters for young pasture. Additionally, the nearly complete disappearance in young pasture, old pasture, and secondary forest sites of a thaumarchaeal genus, the Nitrosotalea, indicates that land-use change can have long lasting effects on large portions of the thaumarchaeal community. The results of this study can be used as a conceptual foundation for determining how ammonia-oxidizers become altered by land-use change in South American tropical forests

Molecular Evidence for Metabolically Active Bacteria in the Atmosphere

Bacterial metabolisms are responsible for critical chemical transformations in nearly all environments, including oceans, freshwater, and soil. Despite the ubiquity of bacteria in the atmosphere, little is known about the metabolic functioning of atmospheric bacterial communities. To gain a better understanding of the metabolism of bacterial communities in the atmosphere, we used a combined empirical and model-based approach to investigate the structure and composition of potentially active bacterial communities in air sampled at a high elevation research station. We found that the composition of the putatively active bacterial community (assayed via rRNA) differed significantly from the total bacterial community (assayed via rDNA). Rare taxa in the total (rDNA) community were disproportionately active relative to abundant taxa, and members of the order Rhodospirillales had the highest potential for activity. We developed theory to explore the effects of random sampling from the rRNA and rDNA communities on observed differences between the communities. We found that random sampling, particularly in cases where active taxa are rare in the rDNA community, will give rise to observed differences in community composition including the occurrence of phantom taxa, taxa which are detected in the rRNA community but not the rDNA community. We show that the use of comparative rRNA/rDNA techniques can reveal the structure and composition of the metabolically active portion of bacterial communities. Our observations suggest that metabolically active bacteria exist in the atmosphere, and that these communities may be involved in the cycling of organic compounds in the atmosphere

Conversion of Amazon rainforest to agriculture alters community traits of methane-cycling organisms

Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here, we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane‐cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane‐cycling microorganisms responded to land use change, with the strongest responses exhibited by methane‐consuming, rather than methane‐producing, microorganisms. These responses included a reduction in the relative abundance of methanotrophs and a significant decrease in the abundance of genes encoding particulate methane monooxygenase. We also observed compositional changes to methanotroph and methanogen communities as well as changes to methanotroph life history strategies. Our observations suggest that methane‐cycling microorganisms are vulnerable to land use change, and this vulnerability may underlie the response of methane flux to land use change in Amazon soils