Microbial ecosystems as targets for improving pig gut health

To date, our understanding of the organisms which constitute the microbiomes of humans and our domesticated species has been limited by the technologies available to study them. Progress from culture to species-based DNA approaches has allowed us to appreciate the scale of animal microbiomes and the changes which can occur over time and space. However, in order to design and validate rational approaches to manipulating microbiomes to optimise health, welfare and productivity, we need to begin to understand them as ecosystems, in which the host and a complex mixture of micro-organisms are continuously engaged both in co-operation to produce resources from food and in competition for those resources. The application of ecological principles can guide this understanding, but we need to validate the concepts we use, since they may not all be as applicable as they might seem.

Nitrogen Isotope Discrepancy Between Primary Producers and Sediments in an Anoxic and Alkaline Lake

Nitrogen isotope compositions (δ15N) in sedimentary rocks are extensively used to investigate the biogeochemical nitrogen cycle through geological times. This use relies on the observation that, in modern continental platforms and anoxic basins, surface sediments faithfully record the δ15N of primary producers, assuming that it was similar in the past. Over Earth’s history, however, surface environments experienced profound changes, including the transition of ammonium-dominated to nitrate-dominated waters and the transition from exclusively microbial ecosystems to ecosystems including multicellularity, which make modern environments significantly different compared to earlier ones, potentially invalidating the fundamental assumption that surface sediments faithfully record the δ15N of primary producers. In order to improve our understanding of the nitrogen isotopic information contained in the early Earth’s sedimentary rock record, we investigate here the nitrogen isotope systematics in a microbial, nitrate free and ammonium-rich modern system, the Dziani Dzaha Lake. In this modern system, the δ15N of the reduced dissolved inorganic nitrogen (i.e., NH4+ and NH3) in the water column is close to ∼7‰ . δ15N of suspended particulate matter (SPM) show a similar average value in surface waters (i.e., where SPM is massively composed of active primary producers), but increases up to 14‰ in the deeper part of the water column during periods when it is enriched in dissolved reduced species (i.e., CH4, H2S/HS− and NH4+/NH3). Surface sediments δ15N, with values comprised between 10 and 14 ‰, seem to preferentially record these positive isotopic signatures, rather than those of active primary producers. We propose here that the observed isotopic pattern is mainly linked to the assimilation of ammonium strongly enriched in 15N by isotope exchange with ammonia under basic conditions. Although ammonium assimilation seems here to be responsible for a significant isotopic enrichment due to the basic conditions, in neutral anoxic environments inhabited by similar microbial ecosystems, this process may also significantly impact the δ15N of primary producers towards more negative values. This would have strong implications for our interpretation of the Precambrian sedimentary record as this finding challenges one the fundamental hypotheses underlying the use of sedimentary δ15N in paleo-oceanographic reconstructions, i.e. that surface sediments faithfully record the δ15N of active primary producers in the photic zone.

Emergent Diversity and Persistent Turnover in Evolving Microbial Cross-Feeding Networks

A distinguishing feature of many ecological networks in the microbial realm is the diversity of substrates that could potentially serve as energy sources for microbial consumers. The microorganisms are themselves the agents of compound diversification via metabolite excretion or overflow metabolism. It has been suggested that the emerging richness of different substrates is an important condition for the immense biological diversity in microbial ecosystems. In this work, we study how complex cross-feeding networks (CFN) of microbial species may develop from a simple initial community given some elemental evolutionary mechanisms of resource-dependent speciation and extinctions using a network flow model. We report results of several numerical experiments and report an in-depth analysis of the evolutionary dynamics. We find that even in stable environments, the system is subject to persisting turnover, indicating an ongoing co-evolution. Further, we compare the impact of different parameters, such as the ratio of mineralization, as well as the metabolic versatility and variability on the evolving community structure. The results imply that high microbial and molecular diversity is an emergent property of evolution in cross-feeding networks, which affects transformation and accumulation of substrates in natural systems, such as soils and oceans, with potential relevance to biotechnological applications.

Looking through the FOG: microbiome characterization and lipolytic bacteria isolation from a fatberg site

Sewer systems are complex physical, chemical and microbial ecosystems where fats, oils and grease (FOG) present a major problem for sewer management. Their accumulation can lead to blockages (‘Fatbergs’), sewer overflows and disruption of downstream wastewater treatment. Further advancements of biological FOG treatments need to be tailored to degrade the FOG, and operate successfully within the sewer environment. In this study we developed a pipeline for isolation of lipolytic strains directly from two FOG blockage sites in the UK, and isolated a range of highly lipolytic bacteria. We selected the five most lipolytic strains using Rhodamine B agar plates and pNP-Fatty acid substrates, with two Serratia spp., two Klebsiella spp. and an environmental Acinetobacter strain that all have the capacity to grow on FOG-based carbon sources. Their genome sequences identified the genetic capacity for fatty acid harvesting (lipases), catabolism and utilization (Fad genes). Furthermore, we performed a preliminary molecular characterization of the microbial community at these sites, showing a diverse community of environmental bacteria at each site, but which did include evidence of sequences related to our isolates. This study provides proof of concept to isolation strategies targeting Fatberg sites to yield candidate strains with bioremediation potential for FOG in the wastewater network. Our work sets the foundation for development of novel bioadditions tailored to the environment with non-pathogenic Acinetobacter identified as a candidate for this purpose.

iVirus 2.0: Cyberinfrastructure-supported tools and data to power DNA virus ecology

Microbes drive myriad ecosystem processes, but under strong influence from viruses. Because studying viruses in complex systems requires different tools than those for microbes, they remain underexplored. To combat this, we previously aggregated double-stranded DNA (dsDNA) virus analysis capabilities and resources into ‘iVirus’ on the CyVerse collaborative cyberinfrastructure. Here we substantially expand iVirus’s functionality and accessibility, to iVirus 2.0, as follows. First, core iVirus apps were integrated into the Department of Energy’s Systems Biology KnowledgeBase (KBase) to provide an additional analytical platform. Second, at CyVerse, 20 software tools (apps) were upgraded or added as new tools and capabilities. Third, nearly 20-fold more sequence reads were aggregated to capture new data and environments. Finally, documentation, as “live” protocols, was updated to maximize user interaction with and contribution to infrastructure development. Together, iVirus 2.0 serves as a uniquely central and accessible analytical platform for studying how viruses, particularly dsDNA viruses, impact diverse microbial ecosystems.

Undervalued Pseudo- nifH Sequences in Public Databases Distort Metagenomic Insights into Biological Nitrogen Fixers

Nitrogen-fixing microbes affect biogeochemical cycling, agricultural productivity, and microbial ecosystems, and their distributions have been investigated intensively using genomic and metagenomic sequencing. Currently, insights into nitrogen fixers in the environment have been acquired by homology searches against nitrogenase genes, particularly the nifH gene, in public databases.

Closed microbial communities self-organize to persistently cycle carbon

Cycles of nutrients (N, P, etc.) and resources (C) are a defining emergent feature of ecosystems. Cycling plays a critical role in determining ecosystem structure at all scales, from microbial communities to the entire biosphere. Stable cycles are essential for ecosystem persistence because they allow resources and nutrients to be regenerated. Therefore, a central problem in ecology is understanding how ecosystems are organized to sustain robust cycles. Addressing this problem quantitatively has proved challenging because of the difficulties associated with manipulating ecosystem structure while measuring cycling. We address this problem using closed microbial ecosystems (CES), hermetically sealed microbial consortia provided with only light. We develop a technique for quantifying carbon cycling in hermetically sealed microbial communities and show that CES composed of an alga and diverse bacterial consortia self-organize to robustly cycle carbon for months. Comparing replicates of diverse CES, we find that carbon cycling does not depend strongly on the taxonomy of the bacteria present. Moreover, despite strong taxonomic differences, self-organized CES exhibit a conserved set of metabolic capabilities. Therefore, an emergent carbon cycle enforces metabolic but not taxonomic constraints on ecosystem organization. Our study helps establish closed microbial communities as model ecosystems to study emergent function and persistence in replicate systems while controlling community composition and the environment.

Late Ediacaran life on land: desiccated microbial mats and large biofilm streamers

The Ediacaran period witnessed transformational change across the Earth–life system, but life on land during this interval is poorly understood. Non-marine/transitional Ediacaran sediments preserve a variety of probable microbially induced sedimentary structures and fossil matgrounds, and the ecology, biogeochemistry and sedimentological impacts of the organisms responsible are now ripe for investigation. Here, we report well-preserved fossils from emergent siliciclastic depositional environments in the Ediacaran of Newfoundland, Canada. These include exquisite, mouldically preserved microbial mats with desiccation cracks and flip-overs, abundant Arumberia -type fossils and, most notably, assemblages of centimetre-to-metre-scale, subparallel, branching, overlapping, gently curving ribbon-like features preserved by aluminosilicate and phosphate minerals, with associated filamentous microfossils. We present morphological, petrographic and taphonomic evidence that the ribbons are best interpreted as fossilized current-induced biofilm streamers, the earliest record of an important mode of life (macroscopic streamer formation) for terrestrial microbial ecosystems today. Their presence shows that late Ediacaran terrestrial environments could produce substantial biomass, and supports recent interpretations of Arumberia as a current-influenced microbial mat fossil, which we here suggest existed on a ‘streamer–arumberiamorph spectrum’. Finally, the absence of classic Ediacaran macrobiota from these rocks despite evidently favourable conditions for soft tissue preservation upholds the consensus that those organisms were exclusively marine.

Emergent phases of ecological diversity and dynamics mapped in microcosms

Natural ecological communities display striking features, such as high biodiversity and a wide range of dynamics, that have been difficult to explain in a unified framework. Using experimental bacterial microcosms, we perform the first direct test of recent complex systems theory predicting that simple aggregate parameters dictate emergent behaviors of the community. As either the number of species or the strength of species interactions is increased, we show that microbial ecosystems transition between distinct qualitative dynamical phases in the predicted order, from a stable equilibrium where all species coexist, to partial coexistence, to emergence of persistent fluctuations in species abundance. Under the same conditions, high biodiversity and fluctuations allow and require each other. Our results demonstrate predictable emergent diversity and dynamics in ecological communities.