Biology subjects

Ladau, J.

Publications and source records attributed to Ladau, J..

8 recordsLinked to original sources

bioRxiv2018

Effect of the macroalgae Asparagopsis taxiformis on methane production and the rumen microbiome assemblage

BackgroundRecent studies using batch-fermentation suggest that the red macroalgae Asparagopsis taxiformis might reduce methane (CH4) emission from beef cattle by up to ~99% when added to rhodes grass hay, a common feed in the Australian beef industry. These experiments have shown significant reductions in methane without compromising other fermentation parameters (i.e. volatile fatty acid production) with A. taxiformis organic matter (OM) inclusion rates of up to 5%. In the study presented here, A. taxiformis was evaluated for its ability to reduce methane production from dairy cattle fed a mixed ration widely utilized in California; the largest milk producer in the US.\n\nResultsFermentation in a semi-continuous in-vitro rumen system suggests that A. taxiformis can reduce methane production from enteric fermentation in dairy cattle by 95% when added at a 5% OM inclusion rate without any obvious negative impacts on volatile fatty acid production. High-throughput 16S ribosomal RNA (rRNA) gene amplicon sequencing showed that seaweed amendment effects rumen microbiome communities consistent with the Anna Karenina hypothesis, with increased beta-diversity, over time scales of approximately three days. The relative abundance of methanogens in the fermentation vessels amended with A. taxiformis decreased significantly compared to control vessels, but this reduction in methanogen abundance was only significant when averaged over the course of the experiment. Alternatively, significant reductions of methane in the A. taxiformis amended vessels was measured in the early stages of the experiment. This suggests that A. taxiformis has an immediate effect on the metabolic functionality of rumen methanogens whereas its impact on microbiome assemblage, specifically methanogen abundance, is delayed.\n\nConclusionsThe methane reducing effect of A. taxiformis during rumen fermentation makes this macroalgae a promising candidate as a biotic methane mitigation strategy in the largest milk producing state in the US. But its effect in-vivo (i.e. in dairy cattle) remains to be investigated in animal trials. Furthermore, to obtain a holistic understanding of the biochemistry responsible for the significant reduction of methane, gene expression profiles of the rumen microbiome and the host animal are warranted.

systems biology↗

bioRxiv2018

Phylogenetically novel uncultured microbial cells dominate Earth microbiomes

To unequivocally determine a microbes physiology, including its metabolism, environmental roles, and growth characteristics, it must be grown in a laboratory culture. Unfortunately, many phylogenetically-novel groups have never been cultured, so their physiologies have only been inferred from genomics and environmental characteristics. Although the diversity, or number of different taxonomic groups, of uncultured clades has been well-studied, their global abundances, or number of cells in any given environment, have not been assessed. We quantified the degree of similarity of 16S rRNA gene sequences from diverse environments in publicly-available metagenome and metatranscriptome databases, which we show are largely free of the culture-bias present in primer-amplified 16S rRNA gene surveys, to their nearest cultured relatives. Whether normalized to scaffold read depths or not, the highest abundance of metagenomic 16S rRNA gene sequences belong to phylogenetically novel uncultured groups in seawater, freshwater, terrestrial subsurface, soil, hypersaline environments, marine sediment, hot springs, hydrothermal vents, non-human hosts, snow and bioreactors (22-87% uncultured genera to classes and 0-64% uncultured phyla). The exceptions were human and human-associated environments which were dominated by cultured genera (45-97%). We estimate that uncultured genera and phyla could comprise 7.3 x 1029 (81%) and 2.2 x 1029 (25%) microbial cells, respectively. Uncultured phyla were over-represented in meta transcript omes relative to metagenomes (46-84% of sequences in a given environment), suggesting that they are viable, and possibly more active than cultured clades. Therefore, uncultured microbes, often from deeply phylogenetically divergent groups, dominate non-human environments on Earth, and their undiscovered physiologies may matter for Earth systems.

microbiology↗

bioRxiv2018

American Gut: an Open Platform for Citizen-Science Microbiome Research

Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the USA, UK, and Australia to one another and to environmental samples. Our results show an unexpected range of beta-diversity in human stool microbiomes as compared to environmental samples, demonstrate the utility of procedures for removing the effects of overgrowth during room-temperature shipping for revealing phenotype correlations, uncover new molecules and kinds of molecular communities in the human stool metabolome, and examine emergent associations among the microbiome, metabolome, and the diversity of plants that are consumed (rather than relying on reductive categorical variables such as veganism, which have little or no explanatory power). We also demonstrate the utility of the living data resource and cross-cohort comparison to confirm existing associations between the microbiome and psychiatric illness, and to reveal the extent of microbiome change within one individual during surgery, providing a paradigm for open microbiome research and education.\n\nImportanceWe show that a citizen-science, self-selected cohort shipping samples through the mail at room temperature recaptures many known microbiome results from clinically collected cohorts and reveals new ones. Of particular interest is integrating n=1 study data with the population data, showing that the extent of microbiome change after events such as surgery can exceed differences between distinct environmental biomes, and the effect of diverse plants in the diet which we confirm with untargeted metabolomics on hundreds of samples.

microbiology↗

bioRxiv2017

The geometry of the distance-decay of similarity in ecological communities

Understanding beta-diversity has strong implications for evaluating the extent of biodiversity and formulating effective conservation policy. Here, we show that the distance-decay relationship, an important measure of beta-diversity, follows a universal form which we call the piecewise quadratic model. To derive the piecewise quadratic model, we develop a new conceptual framework which is based on geometric probability and several key insights about the roles of study design (e.g., plot dimensions and spatial distributions). We fit the piecewise quadratic model to six empirical distance-decay relationships, spanning a range of taxa and spatial scales, including surveys of tropical vegetation, mammals, and amphibians. We find that the model predicts the functional form of the relationships extremely well, with coefficients of determination in excess of 0.95. Moreover, the model predicts a phase transition at distance scales where sample plots are overlapping, which we confirm empirically. Our framework and model provide a fundamental, quantitative link between distance-decay relationships and the shapes of ranges of taxa.

ecology↗

bioRxiv2017

The architecture and design of ecological null models

Many questions in ecology are best addressed using observational data because they concern spatial or temporal scales where experimentation is impractical. Null models, which make predictions in the absence of a particular ecological mechanism, are instrumental for making inferences in these situations, but which null models to use or how to best test them is often unclear; this ambiguity is problematic because different null models and tests can yield different results, suggesting contradictory ecological mechanisms. To address these challenges, this paper presents an overar ching framework for the development and testing of null models, in which desirable models and tests are obtained as solutions to mathematical optimization problems. As an example of how the framework can be applied, this paper shows how it can be used to design null model tests to check for effects of interspecific interactions on species co-occurrence patterns. A minimal sufficient statistic (metric) for effects of interspecific interactions is derived, which achieves the maximal level of data compression without losing information present in the data about interspecific in teractions. Existing, intuitive statistics are shown to lack this property. The paper then derives a statistical hypothesis test that has the greatest possible power (sen sitivity) for detecting effects of competition and facilitation given a controlled false positive rate. This test is shown numerically to improve greatly over existing tests. The optimization paradigm allows the most accurate inferences possible, and should be applicable throughout ecology where null models are used to make inferences.

ecology↗

bioRxiv2017

Four fundamental processes of community assembly

A central aim of ecology is understanding the mechanisms of community assembly. To address this problem, community assembly is often modeled as a sampling process, in which species are selected from a pool of available species, possibly with effects of interspecific interactions, habitat filtering, and other ecological mechanisms. However, the fundamental stochastic sampling process by which species are selected from the pool remains unexplored. Here we demonstrate the distinctness of four canonical sampling processes, the Bernoulli, Plackett-Luce, multinomial, and fractional multinomial processes. Each process can be affected by ecological mechanisms or it can occur in their absence. Although all four of the processes are a priori plausible and the first two are widely used in ecological models, we show that the multinomial and fractional multinomial processes broadly underlie community assembly.

ecology↗

bioRxiv2017

Climate change will lead to pronounced shifts in the diversity of soil microbial communities

Soil bacteria are key to ecosystem function and maintenance of soil fertility. Leveraging associations of current geographic distributions of bacteria with historic climate, we predict that soil bacterial diversity will increase across the majority (~75%) of the Tibetan Plateau and northern North America if bacterial communities equilibrate with existing climatic conditions. This prediction is possible because the current distributions of soil bacteria have stronger correlations with climate from ~50 years ago than with current climate. This lag is likely associated with the time it takes for soil properties to adjust to changes in climate. The predicted changes are location specific and differ across bacterial taxa, including some bacteria that are predicted to have reductions in their distributions. These findings demonstrate the widespread influence that climate change will have on belowground diversity and highlight the importance of considering bacterial communities when assessing climate impacts on terrestrial ecosystems.\n\nIMPORTANCEThere have been many studies highlighting how plant and animal communities lag behind climate change, causing extinction and diversity debts that will slowly be paid as communities equilibrate. By virtue of their short generation times and dispersal abilities, soil bacteria might be expected to respond to climate change quickly and to be effectively in equilibrium with current climatic conditions. We found strong evidence to the contrary in Tibet and North America. These findings could significantly improve understanding of climate impacts on soil microbial communities.

ecology↗

bioRxiv2017

Competition in the savanna: Models of species assemblages in Kruger National Park, South Africa

We examined hypotheses of spatial association arising from direct or indirect competitive interactions, using thirteen years of gridded mammal census data from Kruger National Park, South Africa. As interactions occur at different scales, we explored the data at 1, 5, 10, and 15 km2. We proposed four hypotheses structuring the mammal community: H1. direct competition between carnivores and herbivores; H2-4: indirect competition produced by each of three types of herbivore diet specialization: H2. ruminants and non-ruminants, H3. grazers and browsers, and H4. a four-way division of small and large grazers and browsers. We used the software CoOccur to implement a robus test for evidence of our hypotheses against null models of community assemblage. At 5, 10, and 15km2 scales, the results supported a competition mechanism in the majority of years for hypotheses H1, H3, and H4, and facilitation in H2. At the finest spatial scale (1km2), we saw evidence for a mixture of competitive, neutral and facilitative process. These results suggest strong, large-scale effects of interspecific interactions on distributions of African megafauna, which may not operate at a more local (1km2) scale, underscoring the importance of scale and mechanism in the guild structure of communities.

ecology↗