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Applied Microbiology
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Microbiome in Ecosystem 2.0
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Microbiome in Ecosystem 2.0

A special issue of Applied Microbiology (ISSN 2673-8007).

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 32563

Special Issue Editor

Dr. Bong-Soo Kim

E-Mail Website
Guest Editor
Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon 24252, Republic of Korea
Interests: microbiome; metagenomics; homeostasis; disease; ecosystem
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

This Special Issue is the continuation of our previous special issue "Microbiome in Ecosystem".

Dear Colleagues,

The microbiome consists of complex microbes and related molecules. Recently, the microbiome has been applied to various fields in order to develop a novel way for maintaining homeostasis or the balance of ecosystems. The understanding of the microbiome’s interaction with its habitats including its host is still limited. This Special Issue is devoted to publishing original research and review articles on various aspects of the microbiome in ecosystems. Topics of interest include, but are not restricted to, novel methods for understanding the microbiome, the role of the microbiome in ecosystems, microbe–microbe interactions in the microbiome, microbe–host interactions, and microbe–environment interactions in various ecosystems.

Dr. Bong-Soo Kim
Guest Editor

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. Applied Microbiology is an international peer-reviewed open access quarterly 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 1000 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.

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Published Papers (11 papers)

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Research

Jump to: Review

15 pages, 738 KiB  
Article
Soil Bacteriome Resilience and Reduced Nitrogen Toxicity in Tomato by Controlled Release Nitrogen Fertilizer Compared to Urea
by Carley R. Rohrbaugh, Mary M. Dixon, Jorge A. Delgado, Daniel K. Manter and Jorge M. Vivanco
Appl. Microbiol. 2023, 3(4), 1262-1276; https://doi.org/10.3390/applmicrobiol3040087 - 20 Nov 2023
Viewed by 954
Abstract
Controlled release fertilizers (CRFs) mitigate negative effects of high nitrogen (N) fertilization rates, such as N toxicity and soil N loss. However, it is unknown if potentially toxic rates of CRF and quick release fertilizer differentially affect soil bacterial communities. To examine potential [...] Read more.
Controlled release fertilizers (CRFs) mitigate negative effects of high nitrogen (N) fertilization rates, such as N toxicity and soil N loss. However, it is unknown if potentially toxic rates of CRF and quick release fertilizer differentially affect soil bacterial communities. To examine potential N toxicity effects on soil microbial communities, we grew tomato (Solanum lycopersicum “Rutgers”) for eight weeks in soils that were fertilized with high levels of quick release or controlled release urea and in soils with either low or high initial microbial N competitor populations. In both soils, we observed N toxicity in urea-fertilized tomatoes, but toxicity was ameliorated with CRF application. Controlled release fertilization increased soil N retention, thereby reducing soil N loss. While N toxicity symptoms manifested in the plant, the soil microbiome was only minorly affected. There were subtle differences in soil bacterial populations, in which nitrifying bacteria accumulated in soils fertilized at high N rates, regardless of the type of N fertilizer used. Ultimately, CRF reduced plant N toxicity symptoms but did not change the soil microbiome compared to quick release urea. These results show that while there are clear benefits of CRF regarding N toxicity tolerance on crops, the soil microbiome is resilient to this abiotic stressor. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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17 pages, 1686 KiB  
Article
Impacts of Tillage Practices on Growth, Phosphorus Uptake, and Yield of Maize in Controlled and Field-Based Studies in Relation to Arbuscular Mycorrhizal Fungi
by Yuya Tatewaki, Masao Higo and Katsunori Isobe
Appl. Microbiol. 2023, 3(2), 358-374; https://doi.org/10.3390/applmicrobiol3020025 - 22 Apr 2023
Cited by 1 | Viewed by 1575
Abstract
This study investigated the effects of arbuscular mycorrhizal fungi (AMF) on the growth, phosphorus (P) uptake, and yield of maize in the presence or absence of tillage. The two-year field experiment was conducted in Kanagawa, Japan. Firstly, we investigated whether the presence of [...] Read more.
This study investigated the effects of arbuscular mycorrhizal fungi (AMF) on the growth, phosphorus (P) uptake, and yield of maize in the presence or absence of tillage. The two-year field experiment was conducted in Kanagawa, Japan. Firstly, we investigated whether the presence of indigenous AMF communities in the roots, as determined by amplicon sequencing analysis, contributed to maize growth in Experiment 1, a 2-year field-based study. The findings revealed that the maize (Zea mays L.) in rotary tillage had higher P uptake, growth at the six-leaves collar stage, and yield, compared to no tillage. The AMF communities colonizing maize roots were altered by the presence or absence of tillage; specifically, tillage increased the dominance of the Gigasporaceae, whereas no tillage increased the dominance of the Acaulosporaceae. Based on these findings, we confirmed whether the inoculation of similar AMF strains, as analyzed in the field study of tillage practices on maize roots, produces growth-promoting effects for maize growth in a controlled pot experiment consistent with the results of the field experiment. For experiment 2, Dentiscutata cerradensis TK-1, Cetraspora pellucida SZ-3 (Gigasporaceae), Acaulospora morrowiae AP-5, and A. longula F-1 (Acaulosporaceae) were inoculated as AMF inocula for a pot experiment. The results showed that aboveground biomass did not change with any inoculum compared to the control. The P concentration in maize was higher for D. cerradensis TK-1 and C. pellucida SZ-3 inoculation than for the control. However, inoculation with A. morrowiae AP-5 and A. longula F-1 did not change P concentrations from the control. This indicates that D. cerradensis TK-1 and C. pellucida SZ-3 are more effective in promoting P uptake in maize than in A morrowiae AP-5 and A. longula F-1. Based on field and pot experiments, our findings suggest that tillage practices lead to alterations in the AMF communities that colonize the roots, and this shift may also contribute to changes in P uptake and crop growth. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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13 pages, 2057 KiB  
Article
Characterisation of the Gut Bacteria of Cultured and Wild Spiny Lobster Panulirus ornatus
by Mei C. Ooi, Andrew J. Trotter, Gregory G. Smith and Andrew R. Bridle
Appl. Microbiol. 2023, 3(1), 241-253; https://doi.org/10.3390/applmicrobiol3010016 - 06 Feb 2023
Viewed by 1729
Abstract
The commercial onshore aquaculture of the spiny lobster Panulirus ornatus, while in its infancy, has progressed rapidly from the enabling research that continues at the University of Tasmania. The development of lobster feeds, both fresh and manufactured, has been critical to the [...] Read more.
The commercial onshore aquaculture of the spiny lobster Panulirus ornatus, while in its infancy, has progressed rapidly from the enabling research that continues at the University of Tasmania. The development of lobster feeds, both fresh and manufactured, has been critical to the success of this emerging aquaculture sector. Fresh feeds derived from mussel represent the gold standard in terms of the growth performance of juvenile lobsters. Nonetheless, concerns regarding availability, sustainability, and potential biosecurity issues of fresh feeds highlight the importance of developing manufactured feeds for lobster aquaculture. Wild lobsters are assumed to have a balanced natural diet that allows for standard growth and development, and as such natural diets are often used as a reference for feed development. Similarly, the gut microbiota associated with a natural diet is assumed to reflect a healthy microbial assemblage. The aim of this study was to compare the microbiota of the hindgut and hepatopancreas of cultured P. ornatus fed with a commercial prawn pellet or mussel to that of wild spiny lobster juveniles. Gut samples were analysed using Oxford Nanopore 16S rRNA gene sequencing. Based on principal coordinate analysis, the gut bacteria of cultured lobsters were different from the wild juveniles. The core microbiota of the hindgut and hepatopancreas libraries were phyla Proteobacteria (Gamma, Alpha) and Bacteroidetes. Vibrio was the most dominant genus in both organs. The differences in bacterial relative abundance were mainly between cultured (pellet-, mussel-fed) and wild lobsters. In conclusion, bacteria in the cultured lobsters had significantly different profiles to that of the wild juveniles, indicating that current onshore aquaculture practices alter the gut microbiota. A number of different feeding and culture practices may be required if the aim of closed culture practices is to attain a gut microbiota in cultured animals that is representative of that found in wild spiny lobsters. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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10 pages, 1487 KiB  
Article
Comparison of the Gill Microbiome of Retail Oysters from Two Geographical Locations Exhibited Distinct Microbial Signatures: A Pilot Study for Potential Future Applications for Monitoring Authenticity of Their Origins
by Prashant Singh, David Williams, Frank J. Velez and Ravinder Nagpal
Appl. Microbiol. 2023, 3(1), 1-10; https://doi.org/10.3390/applmicrobiol3010001 - 23 Dec 2022
Cited by 3 | Viewed by 2500
Abstract
The oyster industry is a significant component of United States aquaculture and is vulnerable to various food frauds. In addition to species substitution, mislabeling of oyster geographical origin is performed for economic gains. The geographical origin misrepresentations are performed to claim a famed [...] Read more.
The oyster industry is a significant component of United States aquaculture and is vulnerable to various food frauds. In addition to species substitution, mislabeling of oyster geographical origin is performed for economic gains. The geographical origin misrepresentations are performed to claim a famed region of origin known for its unique flavor profile. DNA barcoding is the gold standard method for identifying seafood species but has limited resolution to the species level. This pilot study was conducted to characterize and compare the oyster gill microbiome as an alternative approach for tracking oysters’ origin. Commercially available raw east coast oysters (Crassostrea virginica) from two distinct geographical locations were purchased. Genomic DNA isolated from the gills was processed for microbiome analysis. The data revealed distinct microbiome signatures among the two sample sets. Oysters from Louisiana showed the presence of eighteen unique bacterial genera, whereas Maryland oysters showed a higher abundance of twelve genera. Findings from this study demonstrate the applicability of microbiome analysis as an emerging alternative approach for identifying geographical origin misrepresentations. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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23 pages, 4521 KiB  
Article
Forensic Analysis of Novel SARS2r-CoV Identified in Game Animal Datasets in China Shows Evolutionary Relationship to Pangolin GX CoV Clade and Apparent Genetic Experimentation
by Adrian Jones, Steven E. Massey, Daoyu Zhang, Yuri Deigin and Steven C. Quay
Appl. Microbiol. 2022, 2(4), 882-904; https://doi.org/10.3390/applmicrobiol2040068 - 07 Nov 2022
Viewed by 9528
Abstract
Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University [...] Read more.
Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University in 2022, and find that sections of the partial genome phylogenetically group with Guangxi pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, it is also found in 10 additional NGS datasets from 5 separate mammalian species and is likely related to contamination by a laboratory researched virus. Absence of bat mitochondrial sequences from the datasets, the fragmentary nature of the virus sequence and the presence of a partial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has been cloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated with significant Homo sapiens genetic material, and numerous viruses not associated with the host animals sampled. We further identify the dominant human haplogroup of the contaminating H. sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association of this novel SARS2r-CoV with both bat CoV and the GX PCoV clades is an important step towards identifying the origin of the GX PCoVs. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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Review

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37 pages, 1024 KiB  
Review
The Vaginal Microbiome during Pregnancy in Health and Disease
by George L. Mendz
Appl. Microbiol. 2023, 3(4), 1302-1338; https://doi.org/10.3390/applmicrobiol3040089 - 30 Nov 2023
Viewed by 1642
Abstract
This study appraises the progress in the understanding of the composition of the vaginal microflora with a focus on the microbiome during pregnancy. This knowledge is presented with the background of the global health contribution, along with the importance of these microbial communities [...] Read more.
This study appraises the progress in the understanding of the composition of the vaginal microflora with a focus on the microbiome during pregnancy. This knowledge is presented with the background of the global health contribution, along with the importance of these microbial communities to pregnancy. A brief review of current methods employed to investigate the structure of these microbial populations is included. Two types of studies, cross-sectional and longitudinal, have been used to characterise the vaginal microbiota; both types are reviewed since they provide information that serves to piece together a more complete picture of the vaginal microflora and its changes during pregnancy. The identity of microbes present in the vagina are examined in the context of health and disease, and, more specifically, in the setting of pregnancy outcomes. The protective role of lactobacilli in maintaining a healthy vaginal environment is evaluated, with analyses of the different roles of various Lactobacillus spp. Classifications of the vaginal microbiota into vagitypes in non-pregnant and pregnant women are discussed. The associations of specific taxa with three adverse pregnancy results, namely, miscarriage, stillbirth, and preterm birth, are examined in some detail. Longitudinal studies investigating changes in the bacterial community composition and taxa abundance demonstrate that this microbiota decreases in richness and diversity relative to those present in non-pregnant microbiomes. Notwithstanding the significant effort made to characterise the vagina bacterial microbiota, a large number of issues remain to be fully understood. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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11 pages, 889 KiB  
Review
Reviewing the Current Understanding of Replant Syndrome in Orchards from a Soil Microbiome Perspective
by Derek R. Newberger, Daniel K. Manter and Jorge M. Vivanco
Appl. Microbiol. 2023, 3(3), 856-866; https://doi.org/10.3390/applmicrobiol3030059 - 04 Aug 2023
Viewed by 1149
Abstract
Replant syndrome (RS) of fruit and nut trees causes reduced tree vigor and crop productivity in orchard systems due to repeated plantings of closely related tree species. Although RS etiology has not been clearly defined, the causal agents are thought to be a [...] Read more.
Replant syndrome (RS) of fruit and nut trees causes reduced tree vigor and crop productivity in orchard systems due to repeated plantings of closely related tree species. Although RS etiology has not been clearly defined, the causal agents are thought to be a complex of soil microorganisms combined with abiotic factors and susceptible tree genetics. Different soil disinfection techniques alleviate RS symptoms by reducing the loads of the deleterious microbiome; however, the positive effect on crop growth is temporary. The goals of this paper are: (1) to conceptualize the establishment of the syndrome from a microbiome perspective and (2) to propose sustainable solutions to develop a beneficial microbiome to inhibit the onset of RS. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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17 pages, 369 KiB  
Review
Univariate and Multivariate Statistical Analysis of Microbiome Data: An Overview
by Hani Aldirawi and Franceskrista G. Morales
Appl. Microbiol. 2023, 3(2), 322-338; https://doi.org/10.3390/applmicrobiol3020023 - 27 Mar 2023
Cited by 2 | Viewed by 2916
Abstract
Microbiome data is high dimensional, sparse, compositional, and over-dispersed. Therefore, modeling microbiome data is very challenging and it is an active research area. Microbiome analysis has become a progressing area of research as microorganisms constitute a large part of life. Since many methods [...] Read more.
Microbiome data is high dimensional, sparse, compositional, and over-dispersed. Therefore, modeling microbiome data is very challenging and it is an active research area. Microbiome analysis has become a progressing area of research as microorganisms constitute a large part of life. Since many methods of microbiome data analysis have been presented, this review summarizes the challenges, methods used, and the advantages and disadvantages of those methods, to serve as an updated guide for those in the field. This review also compared different methods of analysis to progress the development of newer methods. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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29 pages, 1926 KiB  
Review
Microbial Translocation Disorders: Assigning an Etiology to Idiopathic Illnesses
by Adonis Sfera, Sabine Hazan, Carolina Klein, Carlos Manuel Zapata-Martín del Campo, Sarvin Sasannia, Johnathan J. Anton, Leah Rahman, Christina V. Andronescu, Dan O. Sfera, Zisis Kozlakidis and Garth L. Nicolson
Appl. Microbiol. 2023, 3(1), 212-240; https://doi.org/10.3390/applmicrobiol3010015 - 28 Jan 2023
Cited by 2 | Viewed by 3378
Abstract
Gut microbes are immunologically tolerated in the gastrointestinal tract but trigger aggressive immune responses upon translocation across the gut barrier. Although oral tolerance, a physiological process that dampens immune responses to food proteins and commensal microbiota, remains poorly defined, significant progress was made [...] Read more.
Gut microbes are immunologically tolerated in the gastrointestinal tract but trigger aggressive immune responses upon translocation across the gut barrier. Although oral tolerance, a physiological process that dampens immune responses to food proteins and commensal microbiota, remains poorly defined, significant progress was made during and after the Human Immunodeficiency Virus epidemic in the 1980s and the discovery of regulatory T cells in 1995. Additional insight was gained after the discoveries of innate lymphoid cells in 2008 and the functional elucidation of mucosal mast cells. Prior to the historical discovery of human pathogens, the etiologies of most human diseases were considered unknown. The same was true about many genetic disorders prior to the Human Genome Project. Here, we hypothesize that many of the remaining idiopathic conditions, including autoimmune, fibroproliferative, and neuropsychiatric diseases as well as some cancers, can be considered microbial translocation disorders triggered by the host immune responses to extraintestinal gut microbes and/or their constituent parts. In addition to microbial translocation, we also discuss potential interventions for intestinal barrier rehabilitation, including antibodies against tumor necrosis factor-like ligand 1A and membrane lipid replacement supplements. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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24 pages, 680 KiB  
Review
The Importance of the Microbiota in Shaping Women’s Health—The Current State of Knowledge
by Karolina Krupa-Kotara, Paulina Helisz, Weronika Gwioździk and Mateusz Grajek
Appl. Microbiol. 2023, 3(1), 11-34; https://doi.org/10.3390/applmicrobiol3010002 - 26 Dec 2022
Cited by 1 | Viewed by 2047
Abstract
According to current knowledge, a properly colonized human microbiota contributes to the proper functioning of the body. The composition of the natural flora changes depending on age, health, living conditions, and the use of antimicrobial agents: antibiotics, disinfectants, and some cosmetics. The human [...] Read more.
According to current knowledge, a properly colonized human microbiota contributes to the proper functioning of the body. The composition of the natural flora changes depending on age, health, living conditions, and the use of antimicrobial agents: antibiotics, disinfectants, and some cosmetics. The human body is diversely populated with microorganisms and undergoes constant changes under the influence of various factors, and its proper composition is extremely important for the proper functioning of the body. Given the above, it was decided that we would review current scientific research that explains the cause–effect relationship between the composition of microorganisms populating the human body and health, focusing on women’s health. As a result, an overview paper was prepared based on 109 scientific sources from 2009–2022. Special attention was paid to the most recent scientific studies of the last five years, which account for more than 75% of the cited sources. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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12 pages, 1223 KiB  
Review
Impacts of the Green Revolution on Rhizosphere Microbiology Related to Nutrient Acquisition
by Mary Dixon, Carley Rohrbaugh, Antisar Afkairin and Jorge Vivanco
Appl. Microbiol. 2022, 2(4), 992-1003; https://doi.org/10.3390/applmicrobiol2040076 - 30 Nov 2022
Cited by 3 | Viewed by 2903
Abstract
The Green Revolution (GR) involved selective breeding of cereals and the use of high fertilizer inputs with the goal of increasing crop yields to alleviate hunger. As a result of both greater use of inorganic fertilizers and the introduction of semi-dwarf cultivars, grain [...] Read more.
The Green Revolution (GR) involved selective breeding of cereals and the use of high fertilizer inputs with the goal of increasing crop yields to alleviate hunger. As a result of both greater use of inorganic fertilizers and the introduction of semi-dwarf cultivars, grain yield increased globally and hunger was alleviated in certain areas of the world. However, these changes in varietal selection and fertilization regimes have impacted soil fertility and the root-associated microbiome. Higher rates of inorganic fertilizer application resulted in reduced rhizosphere microbial diversity, while semi-dwarf varieties displayed a greater abundance of rhizosphere microbes associated with nitrogen utilization. Ultimately, selection for beneficial aboveground traits during the GR led to healthier belowground traits and nutrient uptake capabilities. Full article
(This article belongs to the Special Issue Microbiome in Ecosystem 2.0)
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