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Microbes in Communities—Geobiological Processes, Symbioses, Applications

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Environmental Microbiology".

Deadline for manuscript submissions: closed (31 July 2020) | Viewed by 42276

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Dr. Michael Hoppert

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Institute of Microbiology and Genetics, University of Goettingen, Grisebachstraße 8, 37077 Göttingen, Germany
Interests: geomicrobiology (microbial marine symbioses, aerophytic biofilms); cytology of prokaryotes
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Prof. Dr. Joachim Reitner

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Geoscience Centre, Geobiology, University of Goettingen, Goldschmidtstraße 3, 37077 Göttingen, Germany
Interests: Geobiology of prebiotic and early life processes Biogeochemistry of biomineralisation; biofilms Microbial mats; Phylogeny and biogeochemistry of ancestral metazoans (sponges, cnidarians)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

All microorganisms—prokaryotes as well as eukaryotes—live in multi-species assemblages. Though these communities are nowadays easy to elucidate (in terms of species diversity) by next-generation sequencing, their functionality is difficult to understand. Knowledge on metabolic properties and flows of substrates and products is lagging behind the fast-growing metagenome data, revealing more and more microbial taxa of an unknown function. Reasons for the occurrence of specific organisms, their interdependence between species, their fitness, and their adaptations are still largely unknown.

In this Issue, we will shed light on the functionality of microbial communities in geobiological processes at micro- and macroscales. This includes but is not restricted to communities involved in primary production and elemental cycling, mineral dissolution and precipitation, animal–microbe symbioses, the degradation of complex compounds, and bioremediation.

For this Special Issue, we ask for research papers and reviews describing interrelations between community members in microbial consortia. We are interested in extreme habitats and model ecosystems with low diversity, in which few organisms are dominant and processes may be reconstructed. We are also looking for research pointing out key players in complex communities like in soil, marine sediments, or animal microbiomes. We are also interested in the role of (bacterial) viruses in microbial communities.

All methodologies, like (functional) metagenomics, metabolome studies, in situ analyses of parameters (macro- to nanoscale), microbial biomarker tracing, and structure-functional microscopic techniques, are welcome.

PD Dr. Michael Hoppert
Prof. Dr. Joachim Reitner
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Related Special Issue

Microbes in Communities—Geobiological Processes, Symbioses, Applications 2.0 in Microorganisms (5 articles)

Published Papers (10 papers)

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Research

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19 pages, 5649 KiB

Open AccessArticle

Sasso Pisano Geothermal Field Environment Harbours Diverse Ktedonobacteria Representatives and Illustrates Habitat-Specific Adaptations

by Sania Arif, Corinna Willenberg, Annika Dreyer, Heiko Nacke and Michael Hoppert

Microorganisms 2021, 9(7), 1402; https://doi.org/10.3390/microorganisms9071402 - 29 Jun 2021

Cited by 5 | Viewed by 2370

Abstract

The hydrothermal steam environment of Sasso Pisano (Italy) was selected to investigate the associated microbial community and its metabolic potential. In this context, 16S and 18S rRNA gene partial sequences of thermophilic prokaryotes and eukaryotes inhabiting hot springs and fumaroles as well as mesophilic microbes colonising soil and water were analysed by high-throughput amplicon sequencing. The eukaryotic and prokaryotic communities from hot environments clearly differ from reference microbial communities of colder soil sites, though Ktedonobacteria showed high abundances in various hot spring samples and a few soil samples. This indicates that the hydrothermal steam environments of Sasso Pisano represent not only a vast reservoir of thermophilic but also mesophilic members of this Chloroflexi class. Metabolic functional profiling revealed that the hot spring microbiome exhibits a higher capability to utilise methane and aromatic compounds and is more diverse in its sulphur and nitrogen metabolism than the mesophilic soil microbial consortium. In addition, heavy metal resistance-conferring genes were significantly more abundant in the hot spring microbiome. The eukaryotic diversity at a fumarole indicated high abundances of primary producers (unicellular red algae: Cyanidiales), consumers (Arthropoda: Collembola sp.), and endoparasite Apicomplexa (Gregarina sp.), which helps to hypothesise a simplified food web at this hot and extremely nutrient-deprived acidic environment. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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20 pages, 4677 KiB

Open AccessArticle

Cyanobacterial Mats in Calcite-Precipitating Serpentinite-Hosted Alkaline Springs of the Voltri Massif, Italy

by Aysha Kamran, Kathrin Sauter, Andreas Reimer, Theresa Wacker, Joachim Reitner and Michael Hoppert

Microorganisms 2021, 9(1), 62; https://doi.org/10.3390/microorganisms9010062 - 29 Dec 2020

Cited by 9 | Viewed by 3496

Abstract

(1) Background: Microbial communities in terrestrial, calcifying high-alkaline springs are not well understood. In this study, we investigate the structure and composition of microbial mats in ultrabasic (pH 10–12) serpentinite springs of the Voltri Massif (Italy). (2) Methods: Along with analysis of chemical and mineralogical parameters, environmental DNA was extracted and subjected to analysis of microbial communities based upon next-generation sequencing. (3) Results: Mineral precipitation and microbialite formation occurred, along with mat formation. Analysis of the serpentinite spring microbial community, based on Illumina sequencing of 16S rRNA amplicons, point to the relevance of alkaliphilic cyanobacteria, colonizing carbonate buildups. Cyanobacterial groups accounted for up to 45% of all retrieved sequences; 3–4 taxa were dominant, belonging to the filamentous groups of Leptolyngbyaceae, Oscillatoriales, and Pseudanabaenaceae. The cyanobacterial community found at these sites is clearly distinct from creek water sediment, highlighting their specific adaptation to these environments. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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15 pages, 1976 KiB

Open AccessArticle

Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx

by Stephanie Serena Schäpe, Jannike Lea Krause, Rebecca Katharina Masanetz, Sarah Riesbeck, Robert Starke, Ulrike Rolle-Kampczyk, Christian Eberlein, Hermann-Josef Heipieper, Gunda Herberth, Martin von Bergen and Nico Jehmlich

Microorganisms 2020, 8(9), 1436; https://doi.org/10.3390/microorganisms8091436 - 19 Sep 2020

Cited by 9 | Viewed by 3202

Abstract

Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the microbiome has already been reported, but little is known on how BPS affects bacterial activity and function. To analyze these effects, we cultivated the simplified human intestinal microbiota (SIHUMIx) in bioreactors at a concentration of 45 µM BPS. By determining biomass, growth of SIHUMIx was followed but no differences during BPS exposure were observed. To validate if the membrane composition was affected, fatty acid methyl esters (FAMEs) profiles were compared. Changes in the individual membrane fatty acid composition could not been described; however, the saturation level of the membranes slightly increased during BPS exposure. By applying targeted metabolomics to quantify short-chain fatty acids (SCFA), it was shown that the activity of SIHUMIx was unaffected. Metaproteomics revealed temporal effect on the community structure and function, showing that BPS has minor effects on the structure or functionality of SIHUMIx. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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18 pages, 2769 KiB

Open AccessArticle

Planctomycetes as a Vital Constituent of the Microbial Communities Inhabiting Different Layers of the Meromictic Lake Sælenvannet (Norway)

by Julia E. Storesund, Anders Lanzèn, Eva-Lena Nordmann, Hilde Rief Armo, Olga Maria Lage and Lise Øvreås

Microorganisms 2020, 8(8), 1150; https://doi.org/10.3390/microorganisms8081150 - 29 Jul 2020

Cited by 9 | Viewed by 3892

Abstract

Meromictic lakes are permanently stratified lakes that display steep gradients in salinity, oxygen and sulphur compounds tightly linked to bacterial community structure and diversity. Lake Sælenvannet is a meromictic lake located south of Bergen, Norway. The 26 m deep lake is connected to the open sea and permanently stratified into two layers separated by a chemocline. The upper water layer is brackish with major input from water runoff from the surroundings. The bottom layer consists of old saline water with low or no oxygen concentrations. Bacteria from phylum Planctomycetes are reported to be ubiquitous in lake environments. They are involved in the degradation of complex carbon sources in aquatic environments and are also linked to anaerobic processes such as fermentation and sulphur reduction. To study Planctomycete distribution along a chemical gradient, we sampled the water column throughout Lake Sælenvannet in 2012 and profiled the microbial community using 16S rRNA amplicon sequencing (metabarcoding) with 454 pyrosequencing. Planctomycetes related 16S rRNA gene sequences were found to be present both in the oxic and anoxic parts of the lake and showed an uneven distribution throughout the water column, with the highest relative abundance of 10% found in the saline anoxic layer at 15 m depth. In a follow-up study in 2014, samples from eight different depths were collected for enrichment and isolation of novel Planctomycetes. This study resulted in successful isolation in pure culture of 10 isolates affiliated to four different genera from the family Planctomycetaceae. One strain closely related to Blastopirellula cremea was isolated from 9 m depth, and two novel strains affiliated to the genera Stieleria and Gimesia were isolated at 7 and 9 m depths, respectively. Furthermore, seven isolates with identical 16S rRNA gene sequences were retrieved from seven different depths which varied greatly in salinity and chemical composition. These isolates likely represent a new species affiliated to Rubinisphaera. The adaptation of this novel Planctomycete to water depths spanning the entire chemical gradient could indicate a high phenotypic plasticity and/or a very efficient survival strategy. Overall, our results show the presence of a diverse group of Planctomycetes in Lake Sælenvannet, with a strong potential for novel adaptations to chemical stress factors. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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14 pages, 3560 KiB

Open AccessArticle

Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data

by Xiu Jia, Francisco Dini-Andreote and Joana Falcão Salles

Microorganisms 2020, 8(6), 798; https://doi.org/10.3390/microorganisms8060798 - 26 May 2020

Cited by 11 | Viewed by 4253

Abstract

Quantifying which assembly processes structure microbiomes can assist prediction, manipulation, and engineering of community outcomes. However, the relative importance of these processes might depend on whether DNA or RNA are used, as they differ in stability. We hypothesized that RNA-inferred community responses to (a)biotic fluctuations are faster than those inferred by DNA; the relative influence of variable selection is stronger in RNA-inferred communities (environmental factors are spatiotemporally heterogeneous), whereas homogeneous selection largely influences DNA-inferred communities (environmental filters are constant). To test these hypotheses, we characterized soil bacterial communities by sequencing both 16S rRNA amplicons from the extracted DNA and RNA transcripts across distinct stages of soil primary succession and quantified the relative influence of each assembly process using ecological null model analysis. Our results revealed that variations in α-diversity and temporal turnover were higher in RNA- than in DNA-inferred communities across successional stages, albeit there was a similar community composition; in line with our hypotheses, the assembly of RNA-inferred community was more closely associated with environmental variability (variable selection) than using the standard DNA-based approach, which was largely influenced by homogeneous selection. This study illustrates the need for benchmarking approaches to properly elucidate how community assembly processes structure microbial communities. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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17 pages, 4312 KiB

Open AccessArticle

Siboglinidae Tubes as an Additional Niche for Microbial Communities in the Gulf of Cádiz—A Microscopical Appraisal

by Blanca Rincón-Tomás, Francisco Javier González, Luis Somoza, Kathrin Sauter, Pedro Madureira, Teresa Medialdea, Jens Carlsson, Joachim Reitner and Michael Hoppert

Microorganisms 2020, 8(3), 367; https://doi.org/10.3390/microorganisms8030367 - 05 Mar 2020

Cited by 9 | Viewed by 4545

Abstract

Siboglinids were sampled from four mud volcanoes in the Gulf of Cádiz (El Cid MV, Bonjardim MV, Al Gacel MV, and Anastasya MV). These invertebrates are characteristic to cold seeps and are known to host chemosynthetic endosymbionts in a dedicated trophosome organ. However, little is known about their tube as a potential niche for other microorganisms. Analyses by scanning and transmission electron microscopy showed dense biofilms on the tube in Al Gacel MV and Anastasya MV specimens by prokaryotic cells. Methanotrophic bacteria were the most abundant forming these biofilms as further supported by 16S rRNA sequence analysis. Furthermore, elemental analyses with electron microscopy and energy-dispersive X-ray spectroscopy point to the mineralization and silicification of the tube, most likely induced by the microbial metabolisms. Bacterial and archaeal 16S rRNA sequence libraries revealed abundant microorganisms related to these siboglinid specimens and certain variations in microbial communities among samples. Thus, the tube remarkably increases the microbial biomass related to the worms and provides an additional microbial niche in deep-sea ecosystems. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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12 pages, 1480 KiB

Open AccessArticle

The Roles of Bacteria in Soil Organic Carbon Accumulation under Nitrogen Deposition in Stipa baicalensis Steppe

by Jie Qin, Hongmei Liu, Jianning Zhao, Hui Wang, Haifang Zhang, Dianlin Yang and Naiqin Zhang

Microorganisms 2020, 8(3), 326; https://doi.org/10.3390/microorganisms8030326 - 26 Feb 2020

Cited by 18 | Viewed by 2878

Abstract

Grassland soil organic carbon (SOC) accounts for 15.5% of the SOC in reservoirs of terrestrial carbon (C) and is a major component of the global C cycle. Current and future reactive N deposited on grassland soils may alter biogeochemical processes and soil microbes. Microorganisms perform most of the decomposition on Earth and shift SOC accumulation. However, how variation in the identity and composition of the bacterial community influences SOC is far from clear. The objective of this study is to investigate the responses of SOC concentration to multiple rates of N addition as well as the roles of bacteria in SOC accumulation. We studied SOC storage and bacterial community composition under N addition treatments (0, 1.5, 3.0, 5.0, 10.0, 15.0, 20.0, and 30.0 g N·m⁻² yr⁻¹) in a 6-yr field experiment in a temperate grassland. We determined the soil inorganic nitrogen concentration and pH in a 0–10 cm soil layer. We used high-throughput genetic sequencing to detect bacteria. N addition led to significant increases in the concentrations of SOC. N addition reduced the soil pH but increased the NO₃-N and NH₄-N levels. The bacterial diversity was highest under low nitrogen addition. N addition increased the relative abundance of Proteobacteria, and Proteobacteria became the second dominant phylum under high N addition. Structural equation modeling further revealed that soil pH and bacterial community structure have an impact on SOC under N deposition. Nitrogen-regulated SOC is associated with Proteobacteria and Planctomycetes. These findings suggest that N deposition may alter the SOC content, highlighting the importance of understanding changes in the bacterial community for soil nutrients under N deposition. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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13 pages, 4511 KiB

Open AccessArticle

Keystone Species and Modularity in Microbial Hydrocarbon Degradation Uncovered by Network Analysis and Association Rule Mining

by Florian Centler, Sarah Günnigmann, Ingo Fetzer and Annelie Wendeberg

Microorganisms 2020, 8(2), 190; https://doi.org/10.3390/microorganisms8020190 - 30 Jan 2020

Cited by 5 | Viewed by 3827

Abstract

Natural microbial communities in soils are highly diverse, allowing for rich networks of microbial interactions to unfold. Identifying key players in these networks is difficult as the distribution of microbial diversity at the local scale is typically non-uniform, and is the outcome of both abiotic environmental factors and microbial interactions. Here, using spatially resolved microbial presence-absence data along an aquifer transect contaminated with hydrocarbons, we combined co-occurrence analysis with association rule mining to identify potential keystone species along the hydrocarbon degradation process. Derived co-occurrence networks were found to be of a modular structure, with modules being associated with specific spatial locations and metabolic activity along the contamination plume. Association rules identify species that never occur without another, hence identifying potential one-sided cross-feeding relationships. We find that hub nodes in the rule network appearing in many rules as targets qualify as potential keystone species that catalyze critical transformation steps and are able to interact with varying partners. By contrasting analysis based on data derived from bulk samples and individual soil particles, we highlight the importance of spatial sample resolution. While individual inferred interactions are hypothetical in nature, requiring experimental verification, the observed global network patterns provide a unique first glimpse at the complex interaction networks at work in the microbial world. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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20 pages, 2979 KiB

Open AccessArticle

Comparative Genomics Reveals Metabolic Specificity of Endozoicomonas Isolated from a Marine Sponge and the Genomic Repertoire for Host-Bacteria Symbioses

by Anoop Alex and Agostinho Antunes

Microorganisms 2019, 7(12), 635; https://doi.org/10.3390/microorganisms7120635 - 30 Nov 2019

Cited by 10 | Viewed by 5673

Abstract

The most recently described bacterial members of the genus Endozoicomonas have been found in association with a wide variety of marine invertebrates. Despite their ubiquity in the host holobiont, limited information is available on the molecular genomic signatures of the symbiotic association of Endozoicomonas with marine sponges. Here, we generated a draft genome of Endozoicomonas sp. OPT23 isolated from the intertidal marine sponge Ophlitaspongia papilla and performed comprehensive comparative genomics analyses. Genome-specific analysis and metabolic pathway comparison of the members of the genus Endozoicomonas revealed the presence of gene clusters encoding for unique metabolic features, such as the utilization of carbon sources through lactate, L-rhamnose metabolism, and a phenylacetic acid degradation pathway in Endozoicomonas sp. OPT23. Moreover, the genome harbors genes encoding for eukaryotic-like proteins, such as ankyrin repeats, tetratricopeptide repeats, and Sel1 repeats, which likely facilitate sponge-bacterium attachment. The genome also encodes major secretion systems and homologs of effector molecules that seem to enable the sponge-associated bacterium to interact with the sponge and deliver the virulence factors for successful colonization. In conclusion, the genome analysis of Endozoicomonas sp. OPT23 revealed the presence of adaptive genomic signatures that might favor their symbiotic lifestyle within the sponge host. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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Review

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10 pages, 275 KiB

Open AccessReview

A Big World in Small Grain: A Review of Natural Milk Kefir Starters

by Fatemeh Nejati, Stefan Junne and Peter Neubauer

Microorganisms 2020, 8(2), 192; https://doi.org/10.3390/microorganisms8020192 - 30 Jan 2020

Cited by 37 | Viewed by 7403

Abstract

Milk kefir is a traditional fermented milk product whose consumption is becoming increasingly popular. The natural starter for kefir production is kefir grain, which consists of various bacterial and yeast species. At the industrial scale, however, kefir grains are rarely used due to their slow growth, complex application, bad reproducibility and high costs. Instead, mixtures of defined lactic acid bacteria and sometimes yeasts are applied, which alter sensory and functional properties compared to natural grain-based milk kefir. In order to be able to mimic natural starter cultures for authentic kefir production, it is a prerequisite to gain deep knowledge about the nature of kefir grains, its microbial composition, morphologic structure, composition of strains on grains and the impact of environmental parameters on kefir grain characteristics. In addition, it is very important to deeply investigate the numerous multi-dimensional interactions among different species, which play important roles on the formation and the functionality of grains. Full article

(This article belongs to the Special Issue Microbes in Communities—Geobiological Processes, Symbioses, Applications)

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