Corrigendum: Exploring the Niche Concept in a Simple Metaorganism

[This corrects the article DOI: 10.3389/fmicb.2020.01942.]

Methane as a source of carbon and energy for chironomid larvae

In recent years it has become increasingly apparent that the microbial loop and microbial production play an important role in many aquatic ecosystems. Microorganisms decompose and thereby recycle organic material in the water column and the sediment, which would otherwise be lost from the food web. Decomposition of organic matter takes place in aerobic and anaerobic sediments of lakes and wetlands, with anaerobic regions representing the sites for methane production. It is estimated that methane oxidising bacteria (MOB, methanotrophs) consume more than 90% of the methane available. Thus, MOB represent a significant pathway for the recycling of methane carbon back into aquatic food webs. Possible sites of trophic transfer are the oxic-anoxic boundary layers in the sediment or the water-sediment interfaces. The results presented in this thesis looked at this specific habitat in lakes. I particularly focused on interactions between sediment-dwelling chironomid larvae and the methane carbon cycle. For the first time I showed experimentally that chironomid larvae can feed directly on MOB biomass and thus include high amounts of methane-derived carbon into their diet. This thesis also emphasises that the contribution of methane carbon to larval diet can vary during the year and is strongly influenced by lake characteristics, specifically by depth. Moreover I applied a multiple stable isotope approach to unravel complexities in benthic food webs. The results of this thesis show that methane is not only an important carbon and energy source for aquatic benthic macroinvertebrates but could also substantially fuel terrestrial and riparian food webs

Enhancing Microbial Pollutant Degradation by Integrating Eco-Evolutionary Principles with Environmental Biotechnology

Highlights: We advocate to shift research efforts in environmental biotechnology from searching for desired traits of monocultures to that of microbial communities. As these traits will be hard to identify with classical genome mining approaches, we recommend using artificial community selection as a tool to identify and to select for novel and/or enhanced functions. Bioremediation and biodegradation with artificially selected microbial communities harbors great potential to become a fast, cost-effective, eco-friendly, and socially acceptable way to remove pollutants without prior knowledge of the involved species and degradation pathways needed. The use of highly integrated multispecies microbial communities instead of monocultures in biodegradation processes will result in more stable and more productive cultures. The novelty of our proposed approach lies in the combination of eco-evolutionary principles with applied biotechnology. This will stimulate new advancements in environmental biotechnology, and will likely result in the discovery of novel metabolic degradation pathways. Environmental accumulation of anthropogenic pollutants is a pressing global issue. The biodegradation of these pollutants by microbes is an emerging field but is hampered by inefficient degradation rates and a limited knowledge of potential enzymes and pathways. Here, we advocate the view that significant progress can be achieved by harnessing artificial community selection for a desired biological process, an approach that makes use of eco-evolutionary principles. The selected communities can either be directly used in bioremediation applications or further be analyzed and modified, for instance through a combination of systems biology, synthetic biology, and genetic engineering. This knowledge can then inform machine learning and enhance the discovery of novel biodegradation pathways

Exploring the niche concept in a simple metaorganism

Organisms and their resident microbial communities - the microbiome - form a complex and mostly stable ecosystem. It is known that the composition of the microbiome and bacterial species abundances can have a major impact on host health and Darwinian fitness, but the processes that lead to these microbial patterns have not yet been identified. We here apply the niche concept and trait-based approaches as a first step in understanding the patterns underlying microbial community assembly and structure in the simple metaorganism Hydra. We find that the carrying capacities in single associations do not reflect microbiota densities as part of the community, indicating a discrepancy between the fundamental and realized niche. Whereas in most cases, the realized niche is smaller than the fundamental one, as predicted by theory, the opposite is observed for Hydra’s two main bacterial colonizers. Both, Curvibacter sp. and Duganella sp. benefit from association with the other members of the microbiome and reach higher fractions as compared to when they are the only colonizer. This cannot be linked to any particular trait that is relevant for interacting with the host or by the utilization of specific nutrients but is most likely determined by metabolic interactions between the individual microbiome members

Microbial Species Coexistence Depends on the Host Environment

Organisms and their resident microbial communities form a complex and mostly stable ecosystem. It is known that the specific composition and abundance of certain bacterial species affect host health and fitness, but the processes that lead to these microbial patterns are unknown. We investigate this by deconstructing the simple microbiome of the freshwater polyp Hydra. We contrast the performance of its two main bacterial associates, Curvibacter and Duganella, on germfree hosts with two in vitro environments over time. We show that interactions within the microbiome but also the host environment lead to the observed species frequencies and abundances. More specifically, we find that both microbial species can only stably coexist in the host environment, whereas Duganella outcompetes Curvibacter in both in vitro environments irrespective of initial starting frequencies. While Duganella seems to benefit through secretions of Curvibacter, its competitive effect on Curvibacter depends upon direct contact. The competition might potentially be mitigated through the spatial distribution of the two microbial species on the host, which would explain why both species stably coexist on the host. Interestingly, the relative abundances of both species on the host do not match the relative abundances reported previously nor the overall microbiome carrying capacity as reported in this study. Both observations indicate that rare microbial community members might be relevant for achieving the native community composition and carrying capacity. Our study highlights that for dissecting microbial interactions the specific environmental conditions need to be replicated, a goal difficult to achieve with in vitro systems

Editorial: The role of dispersal and transmission in structuring microbial communities

Microbial communities influence the systems they inhabit by driving ecosystem processes and promoting the health and fitness of plant and animals hosts. While an extensive body of work has documented variation in microbial community membership across hosts and systems, understanding the drivers of this variation remains a challenge. Much of the focus of these efforts has been on the characterization of host variation or the abiotic environment, and has overlooked the role of dispersal, i.e., the movement of organisms across space, and transmission, i.e., the movement of microbes among environments, hosts and between hosts and their environment

A burst chasing x-ray polarimeter

Gamma-ray bursts are one of the most powerful explosions in the universe and have been detected out to distances of almost 13 billion light years. The exact origin of these energetic explosions is still unknown but the resulting huge release of energy is thought to create a highly relativistic jet of material and a power-law distribution of electrons. There are several theories describing the origin of the prompt GRB emission that currently cannot be distinguished. Measurements of the linear polarization would provide unique and important constraints on the mechanisms thought to drive these powerful explosions. We present the design of a sensitive, and extremely versatile gamma-ray burst polarimeter. The instrument is a photoelectric polarimeter based on a time-projection chamber. The photoelectric time-projection technique combines high sensitivity with broad band-pass and is potentially the most powerful method between 2 and 100 keV where the photoelectric effect is the dominant interaction process. We present measurements of polarized and unpolarized X-rays obtained with a prototype detector and describe the two mission concepts; the Gamma-Ray Burst Polarimeter (GRBP) for the U.S. Naval Academy satellite MidSTAR-2, and the Low Energy Polarimeter (LEP) onboard POET, a broadband polarimetry concept for a small explorer mission

Advancing Our Functional Understanding of Host–Microbiota Interactions: A Need for New Types of Studies

Multicellular life evolved in the presence of microorganisms and formed complex associations with their microbiota, the sum of all associated archaea, bacteria, fungi, and viruses. These associations greatly affect the health and life history of the host, which led to a new understanding of “self” and establishment of the “metaorganism” concept.1 The Collaborative Research Centre (CRC) 1182 aims at elucidating the evolution and function of metaorganisms. Its annual conference, the Young Investigator Research Day (YIRD), serves as a platform for scientists of various disciplines to share novel findings on host–microbiota interactions, thereby providing a comprehensive overview of recent developments and new directions in metaorganism research. Even though we have gained tremendous insights into the composition and dynamics of host‐associated microbial communities and their correlations with host health and disease, it also became evident that moving from correlative toward functional studies is needed to examine the underlying mechanisms of interactions within the metaorganism. Non‐classical model organisms in particular possess significant potential to functionally address many open questions in metaorganism research. Here, we suggest and introduce a roadmap moving from correlation toward a functional understanding of host–microbiota interactions and highlight its potential in emerging ecological, agricultural, and translational medical applications

Regional patterns in the paragenesis and age of inclusions in diamond, diamond composition, and the lithospheric seismic structure of Southern Africa

Abstract The Archean lithospheric mantle beneath the Kaapvaal -Zimbabwe craton of Southern Africa shows F 1% variations in seismic P-wave velocity at depths within the diamond stability field (150 -250 km) that correlate regionally with differences in the composition of diamonds and their syngenetic inclusions. Seismically slower mantle trends from the mantle below Swaziland to that below southeastern Botswana, roughly following the surface outcrop pattern of the Bushveld-Molopo Farms Complex. Seismically slower mantle also is evident under the southwestern side of the Zimbabwe craton below crust metamorphosed around 2 Ga. Individual eclogitic sulfide inclusions in diamonds from the Kimberley area kimberlites, Koffiefontein, Orapa, and Jwaneng have Re -Os isotopic ages that range from circa 2.9 Ga to the Proterozoic and show little correspondence with these lithospheric variations. However, silicate inclusions in diamonds and their host diamond compositions for the above kimberlites, Finsch, Jagersfontein, Roberts Victor, Premier, Venetia, and Letlhakane do show some regional relationship to the seismic velocity of the lithosphere. Mantle lithosphere with slower P-wave velocity correlates with a greater proportion of eclogitic versus peridotitic silicate inclusions in diamond, a greater incidence of younger Sm -Nd ages of silicate inclusions, a greater proportion of diamonds with lighter C isotopic composition, and a lower percentage of low-N diamonds whereas the converse is true for diamonds from higher velocity mantle. The oldest formation ages of diamonds indicate that the mantle keels which became continental nuclei were created by middle Archean (3.2 -3.3 Ga) mantle depletion events with high degrees of melting and early harzburgite formation. The predominance of sulfide inclusions that are eclogitic in the 2.9 Ga age population links late Archean (2.9 Ga) subduction-accretion events involving an oceanic lithosphere component to craton stabilization. These events resulted in a widely distributed younger Archean generation of eclogitic diamonds in the lithospheric mantle. Subsequent Proterozoic tectonic and magmatic event