The microbial rare biosphere: current concepts, methods and ecological principles

2020 ◽  
Author(s):  
Francisco Pascoal ◽  
Rodrigo Costa ◽  
Catarina Magalhães
Keyword(s):  
Community Assembly ◽  
Historical Perspective ◽  
Conceptual Models ◽  
Current Knowledge ◽  
Rare Biosphere ◽  
Ecological Principles ◽  
Integrative View ◽  
Domains Of Life ◽  
And Function ◽  
Microbial Community Assembly

Abstract Our ability to describe the highly diverse pool of low abundance populations present in natural microbial communities is increasing at an unprecedented pace. Yet we currently lack an integrative view of the key taxa, functions, and metabolic activity which make-up this communal pool, usually referred to as the ‘rare biosphere’, across the domains of life. In this context, this review examines the microbial rare biosphere in its broader sense, providing an historical perspective on representative studies which enabled to bridge the concept from macroecology to microbial ecology. It then addresses our current knowledge of the prokaryotic rare biosphere, and covers emerging insights into the ecology, taxonomy, and evolution of low abundance microeukaryotic, viral and host-associated communities. We also review recent methodological advances and provide a synthetic overview on how the rare biosphere fits into different conceptual models used to explain microbial community assembly mechanisms, composition, and function.

scholarly journals A conceptual framework for the phylogenetically constrained assembly of microbial communities

Microbiome ◽  
2019 ◽  
Vol 7 (1) ◽  
Author(s):  
Daniel Aguirre de Cárcer
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Phylogenetic Signal ◽  
A Priori ◽  
Amplicon Sequencing ◽  
Bioinformatic Analysis ◽  
Microbial Ecosystems ◽  
And Function ◽  
Microbial Community Assembly

Abstract Microbial communities play essential and preponderant roles in all ecosystems. Understanding the rules that govern microbial community assembly will have a major impact on our ability to manage microbial ecosystems, positively impacting, for instance, human health and agriculture. Here, I present a phylogenetically constrained community assembly principle grounded on the well-supported facts that deterministic processes have a significant impact on microbial community assembly, that microbial communities show significant phylogenetic signal, and that microbial traits and ecological coherence are, to some extent, phylogenetically conserved. From these facts, I derive a few predictions which form the basis of the framework. Chief among them is the existence, within most microbial ecosystems, of phylogenetic core groups (PCGs), defined as discrete portions of the phylogeny of varying depth present in all instances of the given ecosystem, and related to specific niches whose occupancy requires a specific phylogenetically conserved set of traits. The predictions are supported by the recent literature, as well as by dedicated analyses. Integrating the effect of ecosystem patchiness, microbial social interactions, and scale sampling pitfalls takes us to a comprehensive community assembly model that recapitulates the characteristics most commonly observed in microbial communities. PCGs’ identification is relatively straightforward using high-throughput 16S amplicon sequencing, and subsequent bioinformatic analysis of their phylogeny, estimated core pan-genome, and intra-group co-occurrence should provide valuable information on their ecophysiology and niche characteristics. Such a priori information for a significant portion of the community could be used to prime complementing analyses, boosting their usefulness. Thus, the use of the proposed framework could represent a leap forward in our understanding of microbial community assembly and function.

scholarly journals Metabolic dissimilarity determines the establishment of cross-feeding interactions in bacteria

2020 ◽  
Author(s):  
Samir Giri ◽  
Leonardo Oña ◽  
Silvio Waschina ◽  
Shraddha Shitut ◽  
Ghada Yousif ◽  
...  
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Assembly ◽  
Bacterial Species ◽  
Exchange Interactions ◽  
Structure And Function ◽  
Phylogenetic Distance ◽  
And Function ◽  
Microbial Community Assembly ◽  
Feeding Interactions

AbstractThe exchange of metabolites among different bacterial genotypes is key for determining the structure and function of microbial communities. However, the factors that govern the establishment of these cross-feeding interactions remain poorly understood. While kin selection theory predicts that individuals should direct benefits preferentially to close relatives, the potential benefits resulting from a metabolic exchange may be larger for more distantly related species. Here we distinguish between these two possibilities by performing pairwise cocultivation experiments between auxotrophic recipients and 25 species of potential amino acid donors. Auxotrophic recipients were able to grow in the vast majority of pairs tested (78%), suggesting that metabolic cross-feeding interactions are readily established. Strikingly, both the phylogenetic distance between donor and recipient as well as the dissimilarity of their metabolic networks was positively associated with the growth of auxotrophic recipients. Finally, this result was corroborated in an in-silico analysis of a co-growth of species from a gut microbial community. Together, these findings suggest metabolic cross-feeding interactions are more likely to establish between strains that are metabolically more dissimilar. Thus, our work identifies a new rule of microbial community assembly, which can help predict, understand, and manipulate natural and synthetic microbial systems.SignificanceMetabolic cross-feeding is critical for determining the structure and function of natural microbial communities. However, the rules that determine the establishment of these interactions remain poorly understood. Here we systematically analyze the propensity of different bacterial species to engage in unidirectional cross-feeding interactions. Our results reveal that synergistic growth was prevalent in the vast majority of cases analyzed. Moreover, both phylogenetic and metabolic dissimilarity between donors and recipients favored a successful establishment of metabolite exchange interactions. This work identifies a new rule of microbial community assembly that can help predict, understand, and manipulate microbial communities for diverse applications.

scholarly journals The archaeal RecJ-like proteins: nucleases and ex-nucleases with diverse roles in replication and repair

2018 ◽  
Vol 2 (4) ◽  
pp. 493-501
Author(s):  
Stuart A. MacNeill
Keyword(s):  
Excision Repair ◽  
Current Knowledge ◽  
Nuclease Activity ◽  
Dna Helicase ◽  
Archaeal Species ◽  
Genes Encoding ◽  
Domains Of Life ◽  
Base Excision ◽  
Almost All ◽  
And Function

RecJ proteins belong to the DHH superfamily of phosphoesterases that has members in all three domains of life. In bacteria, the archetypal RecJ is a 5′ → 3′ ssDNA exonuclease that functions in homologous recombination, base excision repair and mismatch repair, while in eukaryotes, the RecJ-like protein Cdc45 (which has lost its nuclease activity) is a key component of the CMG (Cdc45–MCM–GINS) complex, the replicative DNA helicase that unwinds double-stranded DNA at the replication fork. In archaea, database searching identifies genes encoding one or more RecJ family proteins in almost all sequenced genomes. Biochemical analysis has confirmed that some but not all of these proteins are components of archaeal CMG complexes and has revealed a surprising diversity in mode of action and substrate preference. In addition to this, some archaea encode catalytically inactive RecJ-like proteins, and others a mix of active and inactive proteins, with the inactive proteins being confined to structural roles only. Here, I summarise current knowledge of the structure and function of the archaeal RecJ-like proteins, focusing on similarities and differences between proteins from different archaeal species, between proteins within species and between the archaeal proteins and their bacterial and eukaryotic relatives. Models for RecJ-like function are described and key areas for further study highlighted.

scholarly journals Rare Microbial Taxa Emerge When Communities Collide: Freshwater and Marine Microbiome Responses to Experimental Seawater Intrusion

2019 ◽  
Author(s):  
Jennifer D. Rocca ◽  
Marie Simonin ◽  
Justin P. Wright ◽  
Alex Washburne ◽  
Emily Bernhardt
Keyword(s):  
Community Assembly ◽  
Environmental Filtering ◽  
Biotic Interactions ◽  
Structure And Function ◽  
Reciprocal Transplant ◽  
Critical Component ◽  
Central Question ◽  
Marine Communities ◽  
Rare Biosphere ◽  
And Function

AbstractWhole microbial communities regularly merge with one another, often in tandem with their environments, in a process called community coalescence. Such events allow us to address a central question in ecology – what processes shape community assembly. We used a reciprocal transplant and mixing experiment to directly and independently unravel the effects of environmental filtering and biotic interactions on microbiome success when freshwater and marine communities coalesce. The brackish treatment and community mixing resulted in strong convergence of microbiome structure and function toward the marine. Brackish exposure imposed a 96% taxa loss from freshwater and 66% loss from marine microbiomes, which was somewhat counterbalanced by the emergence of tolerant rare taxa. Community mixing further resulted in 29% and 49% loss from biotic interactions between freshwater and marine microbiomes, offset somewhat by mutualistically-assisted rare microbial taxa. Our study emphasizes the importance of the rare biosphere as a critical component of community resilience.

scholarly journals FlowPot axenic plant growth system for microbiota research

2018 ◽  
Author(s):  
James M. Kremer ◽  
Bradley C. Paasch ◽  
David Rhodes ◽  
Caitlin Thireault ◽  
John E. Froehlich ◽  
...  
Keyword(s):  
Microbial Community ◽  
Community Assembly ◽  
Host Factors ◽  
Rigorous Testing ◽  
Microbiome Research ◽  
Growth System ◽  
Microbe Interactions ◽  
And Function ◽  
Microbial Community Assembly ◽  
The Impact

AbstractThe presence of resident microbiota on and inside plants is hypothesized to influence many phenotypic attributes of the host. Likewise, host factors and microbe-microbe interactions are believed to influence microbial community assembly. Rigorous testing of these hypotheses necessitates the ability to grow plants in the absence or presence of resident or defined microbiota. To enable such experiments, we developed the scalable and inexpensive FlowPot growth platform. FlowPots have a sterile peat substrate amenable to colonization by microbiota, and the platform supports growth of the model plant Arabidopsis thaliana in the absence or presence of soil-derived microbial communities. Mechanically, the FlowPot system is unique in that it allows for total-saturation of the sterile substrate by “flushing” with water and/or nutrient solution via an irrigation port. The irrigation port also facilitates passive drainage of the substrate, preventing root anoxia. Materials to construct an individual FlowPot total ∼$2. A simple experiment with 12 FlowPots requires ∼4.5 h of labor following peat and seed sterilization. Plants are grown on FlowPots within a standard tissue culture microbox after inoculation, thus the Flowpot system is modular and does not require a sterile growth chamber. Here, we provide a detailed assembly and microbiota inoculation protocol for the FlowPot system. Collectively, this standardized suite of tools and colonization protocols empowers the plant microbiome research community to conduct harmonized experiments to elucidate the rules microbial community assembly, the impact of microbiota on host phenotypes, and mechanisms by which host factors influence the structure and function of plant microbiota.

scholarly journals H/ACA Small Ribonucleoproteins: Structural and Functional Comparison Between Archaea and Eukaryotes

2021 ◽  
Vol 12 ◽  
Author(s):  
Dominic P. Czekay ◽  
Ute Kothe
Keyword(s):  
Ribosome Biogenesis ◽  
Current Knowledge ◽  
Ribosome Synthesis ◽  
Guide Rnas ◽  
Domains Of Life ◽  
History Of ◽  
And Function ◽  
General Architecture ◽  
Yeast Genetic

During ribosome synthesis, ribosomal RNA is modified through the formation of many pseudouridines and methylations which contribute to ribosome function across all domains of life. In archaea and eukaryotes, pseudouridylation of rRNA is catalyzed by H/ACA small ribonucleoproteins (sRNPs) utilizing different H/ACA guide RNAs to identify target uridines for modification. H/ACA sRNPs are conserved in archaea and eukaryotes, as they share a common general architecture and function, but there are also several notable differences between archaeal and eukaryotic H/ACA sRNPs. Due to the higher protein stability in archaea, we have more information on the structure of archaeal H/ACA sRNPs compared to eukaryotic counterparts. However, based on the long history of yeast genetic and other cellular studies, the biological role of H/ACA sRNPs during ribosome biogenesis is better understood in eukaryotes than archaea. Therefore, this review provides an overview of the current knowledge on H/ACA sRNPs from archaea, in particular their structure and function, and relates it to our understanding of the roles of eukaryotic H/ACA sRNP during eukaryotic ribosome synthesis and beyond. Based on this comparison of our current insights into archaeal and eukaryotic H/ACA sRNPs, we discuss what role archaeal H/ACA sRNPs may play in the formation of ribosomes.

Effects of Maternal Obesity and Gestational Diabetes Mellitus on the Placenta: Current Knowledge and Targets for Therapeutic Interventions

2020 ◽  
Vol 19 (2) ◽  
pp. 176-192
Author(s):  
Samantha Bedell ◽  
Janine Hutson ◽  
Barbra de Vrijer ◽  
Genevieve Eastabrook
Keyword(s):  
Diabetes Mellitus ◽  
Gestational Diabetes ◽  
Gestational Diabetes Mellitus ◽  
Maternal Obesity ◽  
Environmental Changes ◽  
Current Knowledge ◽  
Therapeutic Interventions ◽  
Placental Development ◽  
Exchange Site ◽  
And Function

: Obesity and gestational diabetes mellitus (GDM) are becoming more common among pregnant women worldwide and are individually associated with a number of placenta-mediated obstetric complications, including preeclampsia, macrosomia, intrauterine growth restriction and stillbirth. The placenta serves several functions throughout pregnancy and is the main exchange site for the transfer of nutrients and gas from mother to fetus. In pregnancies complicated by maternal obesity or GDM, the placenta is exposed to environmental changes, such as increased inflammation and oxidative stress, dyslipidemia, and altered hormone levels. These changes can affect placental development and function and lead to abnormal fetal growth and development as well as metabolic and cardiovascular abnormalities in the offspring. This review aims to summarize current knowledge on the effects of obesity and GDM on placental development and function. Understanding these processes is key in developing therapeutic interventions with the goal of mitigating these effects and preventing future cardiovascular and metabolic pathology in subsequent generations.

The Oxford Handbook of the Auditory Brainstem

2018 ◽  
Keyword(s):  
Current Knowledge ◽  
Auditory Pathway ◽  
Auditory Brainstem ◽  
Auditory Midbrain ◽  
Current State ◽  
Neuronal Mechanisms ◽  
Maladaptive Plasticity ◽  
And Function ◽  
Auditory Field

The Oxford Handbook of the Auditory Brainstem provides an in-depth reference to the organization and function of ascending and descending auditory pathways in the mammalian brainstem. Individual chapters are organized along the auditory pathway, beginning with the cochlea and ending with the auditory midbrain. Each chapter provides an introduction to the respective area and summarizes our current knowledge before discussing the disputes and challenges that the field currently faces.The handbook emphasizes the numerous forms of plasticity that are increasingly observed in many areas of the auditory brainstem. Several chapters focus on neuronal modulation of function and plasticity on the synaptic, neuronal, and circuit level, especially during development, aging, and following peripheral hearing loss. In addition, the book addresses the role of trauma-induced maladaptive plasticity with respect to its contribution in generating central hearing dysfunction, such as hyperacusis and tinnitus.The book is intended for students and postdoctoral fellows starting in the auditory field and for researchers of related fields who wish to get an authoritative and up-to-date summary of the current state of auditory brainstem research. For clinical practitioners in audiology, otolaryngology, and neurology, the book is a valuable resource of information about the neuronal mechanisms that are currently discussed as major candidates for the generation of central hearing dysfunction.

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