scholarly journals Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

2018 ◽  
Author(s):  
Robert Marsland ◽  
Wenping Cui ◽  
Joshua Goldford ◽  
Alvaro Sanchez ◽  
Kirill Korolev ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Statistical Physics ◽  
Large Scale ◽  
Species Abundance ◽  
Distinct Species ◽  
Energy Fluxes ◽  
Available Energy ◽  
Resource Limited ◽  
Fundamental Goal ◽  
Ecological Patterns

A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences between the microbes and their chemical environment through the consumption and production of metabolites. By analyzing a generalized consumer resource model that explicitly includes cross-feeding, stochastic colonization, and thermodynamics, we show that complex microbial communities generically exhibit a transition as a function of available energy fluxes from a “resource-limited” regime where community structure and stability is shaped by energetic and metabolic considerations to a diverse regime where the dominant force shaping microbial communities is the overlap between species’ consumption preferences. These two regimes have distinct species abundance patterns, different functional profiles, and respond differently to environmental perturbations. Our model reproduces large-scale ecological patterns observed across multiple experimental settings such as nestedness and differential beta diversity patterns along energy gradients. We discuss the experimental implications of our results and possible connections with disorder-induced phase transitions in statistical physics.

scholarly journals Deterioration-Associated Microbiome of Stone Monuments: Structure, Variation, and Assembly

2018 ◽  
Vol 84 (7) ◽  
Author(s):  
Qiang Li ◽  
Bingjian Zhang ◽  
Xiaoru Yang ◽  
Qinya Ge
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Imaging Techniques ◽  
Bacterial Species ◽  
Species Abundance ◽  
Population Variation ◽  
Structure Variation ◽  
Content Type ◽  
Stone Monuments ◽  
Stone Deterioration

ABSTRACTResearch on the microbial communities that colonize stone monuments may provide a new understanding of stone biodeterioration and microbe-induced carbonate precipitation. This work investigated the seasonal variation of microbial communities in 2016 and 2017, as well as its effects on stone monuments. We determined the bacterial and fungal compositions of 12 samples from four well-separated geographic locations by using 16S rRNA and internal transcribed spacer gene amplicon sequencing.Cyanobacteriaand Ascomycota were the predominant bacterial and fungal phyla, respectively, and differences in species abundance among our 12 samples and 2 years showed no consistent temporal or spatial trends. Alpha diversity, estimated by Shannon and Simpson indices, revealed that an increase or decrease in bacterial diversity corresponded to a decrease or increase in the fungal community from 2016 to 2017. Large-scale association analysis identified potential bacteria and fungi correlated with stone deterioration. Functional prediction revealed specific pathways and microbiota associated with stone deterioration. Moreover, a culture-dependent technique was used to identify microbial isolates involved in biodeterioration and carbonatogenesis; 64% of 85 bacterial isolates caused precipitation of carbonates in biomineralization assays. Imaging techniques including scanning electron microscopy with energy-dispersive spectroscopy, X-ray diffraction, and fluorescence imaging identified CaCO3crystals as calcite and vaterite. Although CaCO3precipitation induced by bacteria often has esthetically deleterious impacts on stone monuments, this process may potentially serve as a novel, environmentally friendly bacterial self-inoculation approach to the conservation of stone.IMPORTANCEComprehensive analyses of the microbiomes associated with the deterioration of stone monuments may contribute to the understanding of mechanisms of deterioration, as well as to the identification of potentially beneficial or undesirable microbial communities and their genomic pathways. In our study, we demonstrated thatCyanobacteriawas the predominant bacterial phylum and exhibited an increase from 2016 to 2017, whileProteobacteriashowed a decreasing trend. Apart from esthetic deterioration caused by cyanobacteria and fungi, white plaque, which is composed mainly of CaCO3and is probably induced byCrossiellaandCyanobacteria, was also considered to be another threat to stone monuments. We showed that there was no significant correlation between microbial population variation and geographic location. Specific functional genes and pathways were also enriched in particular bacterial species. The CaCO3precipitation induced by an indigenous community of carbonatogenic bacteria also provides a self-inoculation approach for the conservation of stone.

scholarly journals Available energy fluxes drive a transition in the diversity, stability, and functional structure of microbial communities

2019 ◽  
Vol 15 (2) ◽  
pp. e1006793 ◽  
Author(s):  
Robert Marsland ◽  
Wenping Cui ◽  
Joshua Goldford ◽  
Alvaro Sanchez ◽  
Kirill Korolev ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Functional Structure ◽  
Energy Fluxes ◽  
Available Energy

scholarly journals Comparative genomics suggests a taxonomic revision of the Staphylococcus cohnii species complex

2021 ◽  
Author(s):  
Anna Lavecchia ◽  
Matteo Chiara ◽  
Caterina De Virgilio ◽  
Caterina Manzari ◽  
Carlo Pazzani ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Species Complex ◽  
Large Scale ◽  
Genomic Sequence ◽  
Bacterial Species ◽  
Taxonomic Revision ◽  
Distinct Species ◽  
The Novel ◽  
Staphylococcus Cohnii ◽  
Taxonomic Assignments

Abstract Staphylococcus cohnii (SC), a coagulase-negative bacterium, was first isolated in 1975 from human skin. Early phenotypic analyses led to the delineation of two subspecies (subsp.), Staphylococcus cohnii subsp. cohnii (SCC) and Staphylococcus cohnii subsp. urealyticus (SCU). SCC was considered to be specific to humans whereas SCU apparently demonstrated a wider host range, from lower primates to humans. The type strains ATCC 29974 and ATCC 49330 have been designated for SCC and SCU, respectively. Comparative analysis of 66 complete genome sequences—including a novel SC isolate—revealed unexpected patterns within the SC complex, both in terms of genomic sequence identity and gene content, highlighting the presence of 3 phylogenetically distinct groups. Based on our observations, and on the current guidelines for taxonomic classification for bacterial species, we propose a revision of the SC species complex. We suggest that SCC and SCU should be regarded as two distinct species: SC and SU (Staphylococcus urealyticus), and that two distinct subspecies, SCC and SCB (SC subsp. barensis, represented by the novel strain isolated in Bari) should be recognized within SC. Furthermore, since large scale comparative genomics studies recurrently suggest inconsistencies or conflicts in taxonomic assignments of bacterial species, we believe that the approach proposed here might be considered for more general application.

Landscape analysis through pictorial transects in degraded lands.

2021 ◽  
Author(s):  
Juan Antonio Campos ◽  
Jaime Villena ◽  
Marta M. Moreno ◽  
Jesús D. Peco ◽  
Mónica Sánchez-Ormeño ◽  
...  
Keyword(s):  
Large Scale ◽  
Fine Particles ◽  
Plant Cover ◽  
Degraded Lands ◽  
Ecological Resources ◽  
Allochthonous Species ◽  
Ecological Patterns ◽  
Good Characterization ◽  
Photosynthetic Potential ◽  
High Degree

<p>Understanding the dynamics of plant populations and their relationship with the characteristics of the terrain (slope, texture, etc.) and with particular phenomena (erosion, pollution, environmental constrains, etc.) that could affect them is crucial in order to manage regeneration and rehabilitation projects in degraded lands. In recent years, the emphasis has been placed on the observation and assessment of microtopographic drivers as they lead to large-scale phenomena. All the ecological variables that affect a given area are interconnected and the success in unraveling the ecological patterns of operation relies on making a good characterization of all the parameters involved.</p><p>It is especially interesting to study the natural colonization processes that take place in Mediterranean areas with a high degree of seasonality, to whose climatic restrictions, the presence of pollutants and various anthropic actions, can be added. Over these degraded areas, we propose using a new tool, what we have come to call "<strong>pictorial transects</strong>", that is, one-dimensional artificial transects built from low-scale photographs (2 m<sup>2</sup>) taken along a line of work (transect) where you can see the points where ecological resources are generated, stored and lost, and their fluctuation throughout time. A derivative of these would be the "<strong>green transects</strong>" in which the green color has been discriminated using the open software Image I. It is an inexpensive, fast and straightforward pictorial method that can be used to research and monitor the spatial and temporal fluctuation of the potential input of resources (organic matter, water, fine particles, etc.) to the ecosystem.</p><p>The information obtained from pictorial transects not only refers to the measurement of the photosynthetic potential per unit area or the location of the critical points (generate, storage or sink of resources) but also makes it possible to monitor the specific composition of the plant cover. For an appropriate use of this methodology, the criteria to determine the direction and length of the different transects must be previously and carefully established according to the objectives proposed in the study. For example: a radial transect in a salty pond will give us information on the changes in the plant cover as we move away from the center and the salinity decreases. In the same pond, a transect parallel to the shore will give us information on those changes that occur in the vegetation that do not depend on the degree of salinity. There are some cases in which this method could be very useful, as in the natural colonization of a degraded mine site or to assess the progression area affected by allochthonous species or weeds in extensive crops.</p>

scholarly journals Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology

2020 ◽  
Vol 2 (2) ◽  
Author(s):  
Pengshuo Yang ◽  
Chongyang Tan ◽  
Maozhen Han ◽  
Lin Cheng ◽  
Xuefeng Cui ◽  
...  
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Network Connectivity ◽  
Small Range ◽  
Environmental Disturbance ◽  
Target Species ◽  
Important Species ◽  
Metagenome Analysis ◽  
Occurrence Patterns ◽  
Edge Networks

Abstract Mainstream studies of microbial community focused on critical organisms and their physiology. Recent advances in large-scale metagenome analysis projects initiated new researches in the complex correlations between large microbial communities. Specifically, previous studies focused on the nodes (i.e. species) of the Species-Centric Networks (SCNs). However, little was understood about the change of correlation between network members (i.e. edges of the SCNs) when the network was disturbed. Here, we introduced a Correlation-Centric Network (CCN) to the microbial research based on the concept of edge networks. In CCN, each node represented a species–species correlation, and edge represented the species shared by two correlations. In this research, we investigated the CCNs and their corresponding SCNs on two large cohorts of microbiome. The results showed that CCNs not only retained the characteristics of SCNs, but also contained information that cannot be detected by SCNs. In addition, when the members of microbial communities were decreased (i.e. environmental disturbance), the CCNs fluctuated within a small range in terms of network connectivity. Therefore, by highlighting the important species correlations, CCNs could unveil new insights when studying not only the functions of target species, but also the stabilities of their residing microbial communities.

scholarly journals Upscaled diurnal cycles of land-atmosphere fluxes: a new global half-hourly data product

2018 ◽  
Author(s):  
Paul Bodesheim ◽  
Martin Jung ◽  
Fabian Gans ◽  
Miguel D. Mahecha ◽  
Markus Reichstein
Keyword(s):  
Data Storage ◽  
Large Scale ◽  
Gross Primary Production ◽  
Net Ecosystem Exchange ◽  
Predictor Variables ◽  
Energy Fluxes ◽  
Diurnal Cycles ◽  
Monthly Average ◽  
Hourly Data ◽  
Data Products

Abstract. Interactions between the biosphere and the atmosphere can be well characterized by fluxes between the two. In particular, carbon and energy fluxes play a major role for understanding biogeochemical processes on ecosystem level or global scale. However, the fluxes can only be measured at individual sites by eddy covariance towers and an upscaling of these local observations is required to analyze global patterns. Previous work focused on upscaling monthly, eight-day, or daily average values and global maps for each flux have been provided accordingly. In this paper, we raise the upscaling of carbon and energy fluxes between land and atmosphere to the next level by increasing the temporal resolution to subdaily scales. We provide continuous half-hourly fluxes for the period from 2001 to 2014 at 0.5◦ spatial resolution, which allows for analyzing diurnal cycles globally. The dataset contains four fluxes: gross primary production (GPP), net ecosystem exchange (NEE), latent heat (LE), and sensible heat (H). We propose two prediction approaches for the diurnal cycles based on large-scale regression models and compare them in extensive cross-validation experiments using different sets of predictor variables. We analyze the results for a set of FLUXNET tower sites showing the suitability of our approaches for this upscaling task. Finally, we have selected one approach to calculate the global half- hourly data products based on predictor variables from remote sensing and meteorology at daily resolution as well as half-hourly potential radiation. In addition, we provide a derived product that only contains monthly average diurnal cycles, which is a lightweight version in terms of data storage that still enables to study the important characteristics of diurnal courses globally. We recommend to primarily use these monthly average diurnal cycles, because they are less affected by the impacts of day-to-day variation, observation noise, and short- term fluctuations on subdaily scales compared to the plain half-hourly flux products. The global half-hourly data products are available at https://doi.org/10.17871/BACI.224.

scholarly journals A residence-time framework for biodiversity

2017 ◽  
Author(s):  
Kenneth J Locey ◽  
Jay T Lennon
Keyword(s):  
Residence Time ◽  
Physical Environment ◽  
Distinct Species ◽  
Ecological Systems ◽  
Complex Environments ◽  
Average Amount ◽  
Resource Limited ◽  
Trade Offs ◽  
Limited Life ◽  
Individual Based Models

Residence time (τ) is the average amount of time that particles spend in an ecosystem. Often estimated from the ratio of volume to flow rate, τ equates the physical environment with dynamics of growth. Here, we propose that τ is key to understanding relationships between biodiversity and the physical ecosystem. We hypothesize that τ acts as a force of selection on traits related to growth and persistence by coupling dispersal and resource supply. We test a suite of predictions using >10,000 stochastic individual-based models that simulate resource-limited life history among ecologically distinct species within complex environments. Predicted relationships between τ and abundance, productivity, and diversity emerged alongside realistic macroecological patterns. Abundance and productivity were greatest when τ equaled an emergent property ϕ, which captures energy-based trade-offs between growth and persistence. From individual metabolism to the dynamics of bioreactors, soils, lakes, and oceans, ecological systems should inherently be governed by τ.

scholarly journals ddRAD Sequencing Sheds Light on Low Interspecific and High Intraspecific mtDNA Divergences in Two Groups of Caddisflies

2021 ◽  
Vol 5 (5) ◽  
Author(s):  
Juha Salokannel ◽  
Kyung Min Lee ◽  
Aki Rinne ◽  
Marko Mutanen
Keyword(s):  
Dna Barcoding ◽  
Large Scale ◽  
Dna Barcode ◽  
Nuclear Genome ◽  
Distinct Species ◽  
Present Species ◽  
Cryptic Diversity ◽  
Weak Support ◽  
Genomic Scale ◽  
Group Species

Abstract Large-scale global efforts on DNA barcoding have repeatedly revealed unexpected patterns of variability in mtDNA, including deep intraspecific divergences and haplotype sharing between species. Understanding the evolutionary causes behind these patterns calls for insights from the nuclear genome. While building a near-complete DNA barcode library of Finnish caddisflies, a case of barcode-sharing and some cases of deep intraspecific divergences were observed. In this study, the Apatania zonella (Zetterstedt, 1840) group and three Limnephilus Leach, 1815 species were studied using double digest RAD sequencing (ddRAD-seq), morphology, and DNA barcoding. The results support the present species boundaries in the A. zonella group species. A morphologically distinct but mitogenetically nondistinct taxon related to parthenogenetic Apatania hispida (Forsslund, 1930) got only weak support for its validity as a distinct species. The morphology and genomic-scale data do not indicate cryptic diversity in any of the three Limnephilus species despite the observed deep intraspecific divergences in DNA barcodes. This demonstrates that polymorphism in mtDNA may not reflect cryptic diversity, but mitonuclear discordance due to other evolutionary causes.

Characterization of microbial communities in exhaust air treatment systems of large-scale pig housing facilities

2010 ◽  
Vol 62 (7) ◽  
pp. 1551-1559 ◽  
Author(s):  
J. Haneke ◽  
N. M. Lee ◽  
T. W. Gaul ◽  
H. F. A. Van den Weghe
Keyword(s):  
Microbial Communities ◽  
Large Scale ◽  
Dust Particles ◽  
Nitrifying Bacteria ◽  
Ammonium Concentration ◽  
Nitrogen Compounds ◽  
Air Treatment ◽  
Fattening Period ◽  
Washing Water ◽  
Housing Facilities

Exhaust air treatment has gained importance as an essential factor in intensive livestock areas due to the rising emissions in the environment. Wet filter walls of multi-stage exhaust air treatment systems precipitate gaseous ammonia and dust particles from exhaust air in washing water. Microbial communities in the biomass developed in the washing water of five large-scale exhaust air treatment units of pig housing facilities, were investigated by fluorescence in situ hybridization (FISH) and 16S rDNA sequence analyses. No “standard” nitrifying bacteria were found in the washing water. Instead mainly α-Proteobacteria, aggregating β- and χ-Proteobacteria, a large number of Actinobacteria, as well as individual Planctomycetales and Crenarchaeota were detected after more than twelve months' operation. The main Proteobacteria species present were affiliated to the families Alcaligenaceae, Comamonadaceae and Xanthomonadaceae. Furthermore, we investigated the consumption of inorganic nitrogen compounds in the washing water of one exhaust air treatment unit during a fattening period with and without pH control. Maintaining the pH at 6.0 resulted in a ca. fivefold higher ammonium concentration and a ca. fourfold lower concentration of oxidized nitrogen compounds after the fattening period was finished.

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