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Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity
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Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity

A special issue of Sustainability (ISSN 2071-1050). This special issue belongs to the section "Environmental Sustainability and Applications".

Deadline for manuscript submissions: closed (30 June 2020) | Viewed by 72103

Special Issue Editor

Prof. Dr. Chien-Sen Liao

E-Mail Website
Guest Editor
Faculty of Department of Medical Science & Biotechnology, College of Medical Science and Technology, I-Shou University, Kaohsiung 82445, Taiwan
Interests: environmental microbiology; environmental toxicology; bioremediation; proteomics; microalgae application
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Of the various ecosystem processes on Earth, nutrient cycling, crop productivity, and control of global warming are among those most important for supporting creatures. Because of the continuous human population growth and food crisis, substantial increases in crop production and sustainable use of soil and aquatic environments will be required. Understanding the factors which control the multiple functions linked to plant production and nutrient cycling under a changing environment is, thus, critical to preserve and manage soil and aquatic ecosystems. We posit that microbial diversity plays a key role in maintaining ecosystem multifunctionality by supporting processes, such as nitrogen fixation, litter decomposition, and organic matter mineralization, which allow the transfer of matter and energy between above- and belowground areas. However, we still have limited knowledge of the relationship between soil microbial diversity and soil/aquatic ecosystem functioning.

Microbial diversity is defined as the number of microbial species within a unit of area. Under the natural climate changes, or in the case of artificial treatments such as the application of biochar into agricultural soils, the soil/aquatic microbial diversity will all be affected. We all know that many environmental microorganisms are not easily obtainable as cultured strains in the laboratory. Hence, molecular bio-techniques, such as denaturing gradient gel electrophoresis (DGGE), terminal restriction fragment length polymorphism (T-RFLP), single-strand conformation polymorphism (SSCP), and next generation sequencing (NGS) have recently been used to study the diversity of microorganisms. These technologies are all for sequencing genomes at a high speed and at a low cost. We invite scholars and researchers to contribute the original research or synthesis papers that deal with recent advances in the relationship between microbial diversity and soil/aquatic ecosystem functioning.

Prof. Dr. Chien-Sen Liao
Guest Editor

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 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.

Keywords

  • Microbial diversity
  • Soil ecosystems
  • Aquatic ecosystems
  • Global warming
  • Biochar application
  • Next generation sequencing

Published Papers (18 papers)

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Research

23 pages, 7672 KiB  
Article
Biodiversity of Microorganisms Colonizing the Surface of Polystyrene Samples Exposed to Different Aqueous Environments
by Tatyana Tourova, Diyana Sokolova, Tamara Nazina, Denis Grouzdev, Eugeni Kurshev and Anatoly Laptev
Sustainability 2020, 12(9), 3624; https://doi.org/10.3390/su12093624 - 30 Apr 2020
Cited by 23 | Viewed by 3352
Abstract
The contamination of marine and freshwater ecosystems with the items from thermoplastics, including polystyrene (PS), necessitates the search for efficient microbial degraders of these polymers. In the present study, the composition of prokaryotes in biofilms formed on PS samples incubated in seawater and [...] Read more.
The contamination of marine and freshwater ecosystems with the items from thermoplastics, including polystyrene (PS), necessitates the search for efficient microbial degraders of these polymers. In the present study, the composition of prokaryotes in biofilms formed on PS samples incubated in seawater and the industrial water of a petrochemical plant were investigated. Using a high-throughput sequencing of the V3–V4 region of the 16S rRNA gene, the predominance of Alphaproteobacteria (Blastomonas), Bacteroidetes (Chryseolinea), and Gammaproteobacteria (Arenimonas and Pseudomonas) in the biofilms on PS samples exposed to industrial water was revealed. Alphaproteobacteria (Erythrobacter) predominated on seawater-incubated PS samples. The local degradation of the PS samples was confirmed by scanning microscopy. The PS-colonizing microbial communities in industrial water differed significantly from the PS communities in seawater. Both communities have a high potential ability to carry out the carbohydrates and amino acids metabolism, but the potential for xenobiotic degradation, including styrene degradation, was relatively higher in the biofilms in industrial water. Bacteria of the genera Erythrobacter, Maribacter, and Mycobacterium were potential styrene-degraders in seawater, and Pseudomonas and Arenimonas in industrial water. Our results suggest that marine and industrial waters contain microbial populations potentially capable of degrading PS, and these populations may be used for the isolation of efficient PS degraders. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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10 pages, 1842 KiB  
Article
Physico-Chemical Aspects and Complete Bacterial Community Composition Analysis of Wasp Nests
by Chaolin Fang and Varenyam Achal
Sustainability 2020, 12(7), 2652; https://doi.org/10.3390/su12072652 - 27 Mar 2020
Cited by 1 | Viewed by 2170
Abstract
Wasps are a group of social insects that build a house, known as a nest, from locally available building materials cemented by their saliva and secretions. Similar to termite nests, there could be many beneficiary bacteria present in their house that can play [...] Read more.
Wasps are a group of social insects that build a house, known as a nest, from locally available building materials cemented by their saliva and secretions. Similar to termite nests, there could be many beneficiary bacteria present in their house that can play an important part in maintaining sustainability in soil ecosystems. Thus, the present study was initiated with a physico-chemical characterization of wasp nests collected from residential and forest zones, followed by unconfined compressive strength (UCS) and X-ray diffraction (XRD) analysis to identify major associated minerals. Further, MiSeq Illumina sequencing of the 16S rRNA gene (V3–V4 regions) was carried out to analyze complete bacterial community composition of wasp nests. The resulting data showed a dominance of Actinobacteria followed by Proteobacteria in both nests. Kaistobacter and Phycicoccus were the dominant genera in each type of wasp nest. It was concluded that wasp nests are an abundant source to isolate bacteria that can potentially be helpful in soil biogeochemical cycling and fertility, antibiotics production and bioremediation. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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27 pages, 4809 KiB  
Article
Ultramicrobacteria from Nitrate- and Radionuclide-Contaminated Groundwater
by Tamara Nazina, Tamara Babich, Nadezhda Kostryukova, Diyana Sokolova, Ruslan Abdullin, Tatyana Tourova, Vitaly Kadnikov, Andrey Mardanov, Nikolai Ravin, Denis Grouzdev, Andrey Poltaraus, Stepan Kalmykov, Alexey Safonov, Elena Zakharova, Alexander Novikov and Kenji Kato
Sustainability 2020, 12(3), 1239; https://doi.org/10.3390/su12031239 - 08 Feb 2020
Cited by 11 | Viewed by 3547
Abstract
The goal of the present work was to investigate the physicochemical and radiochemical conditions and the microbial diversity in groundwater collected near the Lake Karachai (Russia), which was formerly used for the disposal of liquid radioactive waste, to isolate the dominant bacteria, and [...] Read more.
The goal of the present work was to investigate the physicochemical and radiochemical conditions and the microbial diversity in groundwater collected near the Lake Karachai (Russia), which was formerly used for the disposal of liquid radioactive waste, to isolate the dominant bacteria, and to determine their taxonomy and the physiological characteristics responsible for their adaptation to this environment. Groundwater samples contained high concentrations of acetate, oxalate, nitrate, and sulfate, as well as radionuclides. High-throughput sequencing and analysis of the clone libraries revealed lower microbial diversity in the most strongly contaminated groundwater and a predominance of bacteria of the genera Polynucleobacter, Pusillimonas, Candidatus Pelagibacter, and of the candidate phylum Parcubacteria; these groups include species with an ultra small cell size. Archaeal sequences in the libraries belonged to ammonium oxidizers of the phylum Thaumarchaeota and methanogens of the phylum Euryarchaeota. Pure cultures of obligate and facultative ultramicrobacteria belonging to the genera Chryseobacterium, Microbacterium, Salinibacterium, Pusillimonas, Roseomonas, and Janibacter were isolated from water samples. In genomes of Pusillimonas and Roseomonas strains the genes associated with nitrate reduction, resistance to heavy metals and metalloids were revealed. Several isolates are able to participate in the geochemical process of nitrate conversion to N2 using acetate; this results in decreasing redox potential, which in turn may stimulate radionuclide reduction and decrease radionuclide migration in groundwater. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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13 pages, 1392 KiB  
Article
Influence of Repeated Application of Wetting Agents on Soil Water Repellency and Microbial Community
by Enzhan Song, Xiaowei Pan, Robert J. Kremer, Keith W. Goyne, Stephen H. Anderson and Xi Xiong
Sustainability 2019, 11(16), 4505; https://doi.org/10.3390/su11164505 - 20 Aug 2019
Cited by 6 | Viewed by 3489
Abstract
Wetting agents are the primary tool used to control soil water repellency (SWR) and localized dry spot (LDS), especially on sand-based soils. However, the effect of repeated applications of wetting agents on soil microbial populations is unknown. This two-year field experiment investigated six [...] Read more.
Wetting agents are the primary tool used to control soil water repellency (SWR) and localized dry spot (LDS), especially on sand-based soils. However, the effect of repeated applications of wetting agents on soil microbial populations is unknown. This two-year field experiment investigated six wetting agents representing different chemistry effects on a creeping bentgrass (Agrostis stolonifera L.) putting green with existing SWR. Four out of the six wetting agents improved soil volumetric water content in the second growing season, while others showed no effect. This result was negatively correlated to the development of LDS, and positively correlated to occurrence of an air-borne turf disease. Soil microbial populations, determined by soil phospholipid fatty acid (PLFA) analysis, found that none of the treatments applied caused a shift in microbial populations between fungi and bacteria, or gram-positive and gram-negative bacteria. The stress indicators such as saturated to mono-unsaturated fatty acids were not affected by the wetting agents applied as well. However, the wetting agent that contains alkyl block polymers (ABP; Matador) with proven capability for removal of soil organic coatings showed inhibition of microbial populations at one evaluation timing. This result suggested a temporary restriction in soil carbon availability for soil microorganisms following repeated ABP application, which likely contributed to the elevated LDS development observed. Another wetting agent, a combined product of a nonionic surfactant plus acidifiers (NIS; pHAcid), which is designed to reduce inorganic carbonates while enhancing wetting, elevated all soil microbial populations tested at the end of the experiment, indicating a desirable improvement in soil health. However, repeated application of NIS did not reduce SWR at the conclusion of this experiment, which, in combination with a previous report, suggested a minimal disturbance of soil organic coatings of the hydrophobic sand. Overall, this experiment suggested that soil microbial populations can be affected by wetting agents which may further influence SWR, yet the actual effect on soil microorganisms varies depending on the chemistry of the wetting agents. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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16 pages, 4332 KiB  
Article
Biodegradation of Malachite Green in Milkfish Pond Sediments
by Chu-Wen Yang, Wei-Liang Chao, Chi-Yen Hsieh and Bea-Ven Chang
Sustainability 2019, 11(15), 4179; https://doi.org/10.3390/su11154179 - 02 Aug 2019
Cited by 6 | Viewed by 3554
Abstract
Malachite green (MG) is usually applied as a biocide in aquaculture worldwide. The microbial degradation of MG and changes in the microbial community composition of milkfish (Chanos chanos) culture pond sediments were assessed in this study. Three MG-degrading bacteria strains—M6, M10, [...] Read more.
Malachite green (MG) is usually applied as a biocide in aquaculture worldwide. The microbial degradation of MG and changes in the microbial community composition of milkfish (Chanos chanos) culture pond sediments were assessed in this study. Three MG-degrading bacteria strains—M6, M10, and M12—were isolated, identified, and characterized. Strains M6, M10, and M12 are closely related to Zhouia amylolytica, Tenacibaculum mesophilum, and Enterobacter cloacae, respectively. The bacterial strains M10 and M12 showed good ability to degrade MG in the sediment. The MG degradation rate was increased after adding MG three more times. The microbial community in the sediment changes with different treatments. The bacterial strains M10 and M12 provide a potential solution for the treatment of sediment of saline aquaculture ponds with MG contamination. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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20 pages, 8438 KiB  
Article
Changes of Microbial Diversity in Rhizosphere Soils of New Quality Varieties of Winter Wheat Cultivation in Organic Farming
by Anna Gałązka, Emilia Grzęda and Krzysztof Jończyk
Sustainability 2019, 11(15), 4057; https://doi.org/10.3390/su11154057 - 27 Jul 2019
Cited by 12 | Viewed by 2884
Abstract
The aim of this paper was to evaluation functional diversity in rhizosphere soils of new quality varieties of winter wheat cultivation in organic farming. Field experiments were carried out in 2017 and 2018. Twelve commercial winter wheat varieties were selected for testing: Arktis, [...] Read more.
The aim of this paper was to evaluation functional diversity in rhizosphere soils of new quality varieties of winter wheat cultivation in organic farming. Field experiments were carried out in 2017 and 2018. Twelve commercial winter wheat varieties were selected for testing: Arktis, Bellisa, Estivus, Fidelius, Hondia, Jantarka, KWS Ozon, Linus, Markiza, Ostka Strzelecka, Pokusa, and Rokosz. Winter wheat cultivars were chosen for their high yielding potential and good tolerance to fungal diseases. In the plant production conducted in accordance with the principles of organic farming, the selection of the best quality varieties is a key element of agrotechnics. The samples of rhizosphere soils were collected each year in two seasons: spring and summer. The basic parameters of soil biological activities and microbial biodiversity indicators were determined. The high variability of biological activity and functional diversity of rhizosphere soils in the growing season between particular varieties of winter wheat was observed. The rhizosphere soils from varieties such as Bellisa, Arktis, Jantarka, Fidelius, Ostka Strzelecka, Pokusa, Rokosz and KWS Ozon were characterized by high biological activity and functional biodiversity. On the other hand, the soils collected from the varieties Estivus, Fidelius, Jantarkaand Hondia were characterized by medium and low biological activity and biodiversity indices. The highest yield was found in winter wheat varieties such as Bellisa, Fidelius and Jantarka. The results of these analyses allows for a more complete characterization of the yield potential of the tested varieties and their suitability for cultivation in the conditions of organic farming, taking into account the biological activity of soils. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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20 pages, 3981 KiB  
Article
Analysis of Soil Properties, Bacterial Community Composition, and Metabolic Diversity in Fluvisols of a Floodplain Area
by Karolina Furtak, Jarosław Grządziel, Anna Gałązka and Jacek Niedźwiecki
Sustainability 2019, 11(14), 3929; https://doi.org/10.3390/su11143929 - 19 Jul 2019
Cited by 27 | Viewed by 4839
Abstract
The quality of a soil environment affects the microbial community that inhabits it. We decided to examine whether soils formed from river sediments, located in an area of high biodiversity of organisms, are fertile and microbiologically diverse. Fluvisols are considered to be one [...] Read more.
The quality of a soil environment affects the microbial community that inhabits it. We decided to examine whether soils formed from river sediments, located in an area of high biodiversity of organisms, are fertile and microbiologically diverse. Fluvisols are considered to be one of the most fertile soils. In this research, bacterial and metabolic diversity, as well as physico–chemical parameters, in three Fluvisols from the Vistula River Gorge of Lesser Poland was investigated. The analysis of physico–chemical and biological parameters demonstrated statistically significant differences between the three Fluvisols examined. While determining the metabolic potential of soil microbiomes with the use of the EcoPlate™ Biolog® technique, we also noted variation between the Fluvisols; however, they were arranged in a significantly different manner from other properties. The next generation sequencing method enabled us to determine the microorganisms common to three Fluvisols, and we identified bacteria specific to individual soils. These results corresponded with the data obtained through EcoPlate™, indicating that the structural diversity and metabolic potential of the microbiome does not always depend on soil quality parameters. Meanwhile, the increased structural diversity of the microbiome was found to improve the metabolic potential of soil microorganisms. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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14 pages, 1427 KiB  
Article
Variation of Microbial Communities in Aquatic Sediments under Long-Term Exposure to Decabromodiphenyl Ether and UVA Irradiation
by Yi-Tang Chang, Hsi-Ling Chou, Hui Li and Stephen Boyd
Sustainability 2019, 11(14), 3773; https://doi.org/10.3390/su11143773 - 10 Jul 2019
Cited by 8 | Viewed by 2498
Abstract
Abiotic components create different types of environmental stress on bacterial communities in aquatic ecosystems. In this study, the long-term exposure to various abiotic factors, namely a high-dose of the toxic chemical decabromodiphenyl ether (BDE-209), continuous UVA irradiation, and different types of sediment, were [...] Read more.
Abiotic components create different types of environmental stress on bacterial communities in aquatic ecosystems. In this study, the long-term exposure to various abiotic factors, namely a high-dose of the toxic chemical decabromodiphenyl ether (BDE-209), continuous UVA irradiation, and different types of sediment, were evaluated in order to assess their influence on the bacterial community. The dominant bacterial community in a single stress situation, i.e., exposure to BDE-209 include members of Comamonadaceae, members of Xanthomonadaceae, a Pseudomonas sp. and a Hydrogenophaga sp. Such bacteria are capable of biodegrading polybrominated diphenyl ethers (PBDEs). When multiple environmental stresses were present, Acidobacteria bacterium and a Terrimonas sp. were predominant, which equipped the population with multiple physiological characteristics that made it capable of both PBDE biodegradation and resistance to UVA irradiation. Methloversatilis sp. and Flavisolibacter sp. were identified as representative genera in this population that were radioresistant. In addition to the above, sediment heterogeneity is also able to alter bacterial community diversity. In total, seventeen species of bacteria were identified in the microcosms containing more clay particles and higher levels of soil organic matter (SOM). This means that these communities are more diverse than in microcosms that contained more sand particles and a lower SOM, which were found to have only twelve identifiable bacterial species. This is the first report to evaluate how changes in bacterial communities in aquatic sediment are affected by the presence of multiple variable environmental factors at the same time. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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9 pages, 852 KiB  
Article
The Control of Rice Blast Disease by the Novel Biofungicide Formulations
by Wen-Ching Chen, Tai-Ying Chiou, Aileen L. Delgado and Chien-Sen Liao
Sustainability 2019, 11(12), 3449; https://doi.org/10.3390/su11123449 - 23 Jun 2019
Cited by 19 | Viewed by 9485
Abstract
The study aims to develop novel biofungicide formulations against rice blast disease. A total of 300 rhizobacteria strains were isolated from rice field soil and were examined for the inhibition of Magnaporthe oryzae growth in a vitro test. Among them, only six rhizobacteria [...] Read more.
The study aims to develop novel biofungicide formulations against rice blast disease. A total of 300 rhizobacteria strains were isolated from rice field soil and were examined for the inhibition of Magnaporthe oryzae growth in a vitro test. Among them, only six rhizobacteria showed inhibition against M. oryzae. The three strains that showed the highest inhibition were Bacillus subtilis 5, B. cereus 3S5, and Pseudomonas fluorecens 10S2. A rice hull mixture and liquid medium were mixed with the above-mentioned bacterial suspensions into three bacterial formulas and tested separately on the rice cultivar UPLRi-5 after infection by M. oryzae under a controlled condition. The three novel biofungicide formulas significantly inhibited rice blast disease intensity with a mean disease control rate being approximately 31% higher than the control. The formulas proved to be effective and should be considered as promising novel treatments for rice blast disease. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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15 pages, 4003 KiB  
Article
Investigation of a Farm-scale Multitrophic Recirculating Aquaculture System with the Addition of Rhodovulum sulfidophilum for Milkfish (Chanos chanos) Coastal Aquaculture
by Bea-Ven Chang, Chien-Sen Liao, Yi-Tang Chang, Wei-Liang Chao, Shinn-Lih Yeh, Dong-Lin Kuo and Chu-Wen Yang
Sustainability 2019, 11(7), 1880; https://doi.org/10.3390/su11071880 - 28 Mar 2019
Cited by 19 | Viewed by 5907
Abstract
Globally, coastal aquaculture is growing due to the large demand for marine products. Specific impacts caused by coastal aquaculture on the environment include the discharge of culture farm effluents, stress on ground water (the absence of recycling), nutrient pollution, and diseases of cultured [...] Read more.
Globally, coastal aquaculture is growing due to the large demand for marine products. Specific impacts caused by coastal aquaculture on the environment include the discharge of culture farm effluents, stress on ground water (the absence of recycling), nutrient pollution, and diseases of cultured animals. Three methods, integrated multitrophic aquaculture (IMTA), recirculating aquaculture system (RAS), and beneficial bacteria for aquaculture, have been developed to solve these problems. In this study, the advantages of IMTA and RAS were integrated to develop a novel multitrophic recirculating aquaculture system (MRAS) to adapt to the farm-scale culturing of milkfish (Chanos chanos). The photosynthetic bacteria Rhodovulum sulfidophilum was added to enhance the performance of the farm-scale milkfish MRAS. This setting could promote growth of beneficial bacteria, such as the nitrogen cycle-associated microbial community and the anoxygenic phototrophic Acidobacteria community. The ammonia level was reduced, and the total phosphorous level was stable in the water recycled in the MRAS. The cyanobacteria, algae, Vibrio, Escherichia, and other potential pathogenic bacteria communities were inhibited in the MRAS. This study provides an effective design of a water recycling aquaculture system. Milkfish, Asian tiger shrimp (Penaeus monodon), Asian hard clam (Meretrix lusoria), and seaweed (Gracilaria sp.) can be cultured and simultaneously produced in the system. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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13 pages, 1267 KiB  
Article
Screening of Rice Endophytic Biofertilizers with Fungicide Tolerance and Plant Growth-Promoting Characteristics
by Fo-Ting Shen, Jui-Hung Yen, Chien-Sen Liao, Wen-Ching Chen and Yi-Ting Chao
Sustainability 2019, 11(4), 1133; https://doi.org/10.3390/su11041133 - 21 Feb 2019
Cited by 56 | Viewed by 5882
Abstract
The application of pesticides is unavoidable in conventional agricultural practice. To develop effective biofertilizers, bacterial strains with both pesticide tolerance and plant growth-promoting (PGP) traits were isolated for further testing. Seedlings of rice (Oryza sativa) were planted in soil with 1, [...] Read more.
The application of pesticides is unavoidable in conventional agricultural practice. To develop effective biofertilizers, bacterial strains with both pesticide tolerance and plant growth-promoting (PGP) traits were isolated for further testing. Seedlings of rice (Oryza sativa) were planted in soil with 1, 5, or 10 times the recommended rates of the fungicides etridiazole, metalaxyl, and tricyclazole. Endophytic bacteria were isolated from roots of rice seedlings. The bacterial 16S rDNA sequences and related PGP characteristics including potential nitrogen fixation, phosphorus-solubilizing and indole acetic acid (IAA) production ability were further examined. In all, 17 different strains were obtained from rice seedling roots; five strains with both nitrogen fixation potential and IAA production ability included Rhizobium larrymoorei E2, Bacillus aryabhattai E7, Bacillus aryabhattai MN1, Pseudomonas granadensis T6, and Bacillus fortis T9. Except for T9, all strains could tolerate two or more fungicides. We inoculated rice roots with the endophytic bacteria and all conferred rice growth-promoting ability. Bacillus aryabhattai MN1 was further tested and showed high tryptophan dose-dependent IAA production ability, tolerance towards etridiazole and metalaxyl application and should be considered a potential bacterial biofertilizer. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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18 pages, 2269 KiB  
Article
A Comparison of the Microbial Community and Functional Genes Present in Free-Living and Soil Particle-Attached Bacteria from an Aerobic Bioslurry Reactor Treating High-Molecular-Weight PAHs
by Chu-Chun Yu, Ting-Chieh Chang, Chien-Sen Liao and Yi-Tang Chang
Sustainability 2019, 11(4), 1088; https://doi.org/10.3390/su11041088 - 19 Feb 2019
Cited by 10 | Viewed by 2902
Abstract
High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) contaminate a wide range of ecosystems, including soils, groundwater, rivers and harbor sediments. The effective removal of HMW PAHs is a difficult challenge if a rapid remediation time and low economic cost are required. Bioremediation provides a [...] Read more.
High-molecular-weight (HMW) polycyclic aromatic hydrocarbons (PAHs) contaminate a wide range of ecosystems, including soils, groundwater, rivers and harbor sediments. The effective removal of HMW PAHs is a difficult challenge if a rapid remediation time and low economic cost are required. Bioremediation provides a cheap and eco-friendly cleanup strategy for the removal of HMW PAHs. Previous studies have focused on removal efficiency during PAHs bioremediation. In such studies, only limited research has targeted the bacterial communities and functional genes present in such bioremediation systems, specifically those of free-living (aqueous) bacteria and soil particle-attached bacteria present. In this study, a high-level of HMW PAH (1992 mg/kg pyrene) was bioremediated in an aerobic bioslurry reactor (ABR) for 42 days. The results showed a pseudo first order constant rate for pyrene biodegradation of 0.0696 day−1. The microbial communities forming free-living bacteria and soil-attached bacteria in the ABR were found to be different. An analysis of the aqueous samples identified free-living Mycobacterium spp., Pseudomonas putida, Rhodanobacter spp. and Burkholderia spp.; these organisms would seem to be involved in pyrene biodegradation. Various biointermediates, including phenanthrene, catechol, dibenzothiophene, 4,4′-bipyrimidine and cyclopentaphenanthrene, were identified and measured in the aqueous samples. When a similar approach was taken with the soil particle samples, most of the attached bacterial species did not seem to be involved in pyrene biodegradation. Furthermore, community level physiological profiling resulted in significantly different results for the aqueous and soil particle samples. Nevertheless, these two bacterial populations both showed positive signals for the presence of various dioxygenases, including PAHs-RHDα dioxygenases, riesk iron-sulfur motif dioxygenases and catechol 2,3-dioxygenases. The present findings provide a foundation that should help environmental engineers when designing future HMW PAH bioremediation systems that use the ABR approach. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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16 pages, 1402 KiB  
Article
Short-Term Response of the Soil Microbial Abundances and Enzyme Activities to Experimental Warming in a Boreal Peatland in Northeast China
by Yanyu Song, Changchun Song, Jiusheng Ren, Xiuyan Ma, Wenwen Tan, Xianwei Wang, Jinli Gao and Aixin Hou
Sustainability 2019, 11(3), 590; https://doi.org/10.3390/su11030590 - 23 Jan 2019
Cited by 33 | Viewed by 3953
Abstract
Global warming is likely to influence the soil microorganisms and enzyme activity and alter the carbon and nitrogen balance of peatland ecosystems. To investigate the difference in sensitivities of carbon and nitrogen cycling microorganisms and enzyme activity to warming, we conducted three-year warming [...] Read more.
Global warming is likely to influence the soil microorganisms and enzyme activity and alter the carbon and nitrogen balance of peatland ecosystems. To investigate the difference in sensitivities of carbon and nitrogen cycling microorganisms and enzyme activity to warming, we conducted three-year warming experiments in a boreal peatland. Our findings demonstrated that both mcrA and nirS gene abundance in shallow soil and deep soil exhibited insensitivity to warming, while shallow soil archaea 16S rRNA gene and amoA gene abundance in both shallow soil and deep soil increased under warming. Soil pmoA gene abundance of both layers, bacterial 16S rRNA gene abundance in shallow soil, and nirK gene abundance in deep soil decreased due to warming. The decreases of these gene abundances would be a result of losing labile substrates because of the competitive interactions between aboveground plants and underground soil microorganisms. Experimental warming inhibited β-glucosidase activity in two soil layers and invertase activity in deep soil, while it stimulated acid phosphatase activity in shallow soil. Both temperature and labile substrates regulate the responses of soil microbial abundances and enzyme activities to warming and affect the coupling relationships of carbon and nitrogen. This study provides a potential microbial mechanism controlling carbon and nitrogen cycling in peatland under climate warming. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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13 pages, 4640 KiB  
Article
Biodegradation of Tetrabromobisphenol-A in Mangrove Sediments
by Chu-Wen Yang, Chien-Sen Liao, His Ku and Bea-Ven Chang
Sustainability 2019, 11(1), 151; https://doi.org/10.3390/su11010151 - 28 Dec 2018
Cited by 9 | Viewed by 3435
Abstract
Tetrabromobisphenol-A (TBBPA) is a pollutant which has a devastating impact on our environment and should be removed from earth. This research aims to evaluate the aerobic and anaerobic TBBPA degradation and bacterial community changes in mangrove sediments. TBBPA degradation in the sediments was [...] Read more.
Tetrabromobisphenol-A (TBBPA) is a pollutant which has a devastating impact on our environment and should be removed from earth. This research aims to evaluate the aerobic and anaerobic TBBPA degradation and bacterial community changes in mangrove sediments. TBBPA degradation in the sediments was enhanced with a microcapsuled enzyme extract of spent mushroom compost (MC) under aerobic conditions and with zerovalent iron under anaerobic conditions. The TBBPA aerobic or anaerobic degradation rates were enhanced for three time additions. Four bacterial genera (Bacillus, Erythrobacter, Pseudomonas, Rhodococcus) were associated with TBBPA aerobic degradation; and four other bacterial genera (Desulfovibrio, Pseudomonas, Sphaerochaeta, Sphingomonas) were associated with TBBPA anaerobic degradation in the sediment. Moreover, nine methanogens were identified under anaerobic conditions that might also be involved in TBBPA anaerobic degradation in the sediment. Our results demonstrate two feasible methods toward TBBPA bioremediation for mangrove sediments under aerobic and anaerobic conditions. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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17 pages, 4196 KiB  
Article
Community-Level Physiological Profiles of Microorganisms from Different Types of Soil That Are Characteristic to Poland—A Long-Term Microplot Experiment
by Jarosław Grządziel, Karolina Furtak and Anna Gałązka
Sustainability 2019, 11(1), 56; https://doi.org/10.3390/su11010056 - 21 Dec 2018
Cited by 27 | Viewed by 4839
Abstract
Comparative studies, such as the analysis of physicochemical properties and the microbiological composition of soil, are burdened with many problems resulting from the various locations of soils—often, different weather conditions among the experimental fields and varying time between the sample collection and analysis. [...] Read more.
Comparative studies, such as the analysis of physicochemical properties and the microbiological composition of soil, are burdened with many problems resulting from the various locations of soils—often, different weather conditions among the experimental fields and varying time between the sample collection and analysis. The aim of this study was to assess the differences in the physiological profiles of bacterial communities from eight different types of soils from Poland, used in the microplot experiment that was established in 1881. The same plant species were continuously grown at all plots, at the same time, and the soil received the same type of fertilization. Moreover, the soils were always under the same weather conditions. The community-level physiological profiles of microorganisms were evaluated by using the Biolog EcoPlate™ method. The analysis demonstrated that good quality soils, especially the Gleyic Chernozem, Cambic Leptosol, and the Fluvic Cambisol exhibit a significantly higher enzyme activity, compared with the dystric soils. The dehydrogenases activity in the different time-points indicates a wide soil microbiome buffering capacity, which allows the persistence of a relatively permanent physiological profile, over many years. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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13 pages, 3537 KiB  
Article
Influence of Sampling Point Discretization on the Regional Variability of Soil Organic Carbon in the Red Soil Region, China
by Zhongqi Zhang, Yiquan Sun, Dongsheng Yu, Peng Mao and Li Xu
Sustainability 2018, 10(10), 3603; https://doi.org/10.3390/su10103603 - 10 Oct 2018
Cited by 7 | Viewed by 2490
Abstract
Research on the regional variability of soil organic carbon (SOC) has focused mostly on the influence of the number of soil sampling points and interpolation methods. Little attention has typically been paid to the influence of sampling point discretization. Based on dense soil [...] Read more.
Research on the regional variability of soil organic carbon (SOC) has focused mostly on the influence of the number of soil sampling points and interpolation methods. Little attention has typically been paid to the influence of sampling point discretization. Based on dense soil sampling points in the red soil area of Southern China, we obtained four sample discretization levels by a resampling operation. Then, regional SOC distributions were obtained at four levels by two interpolation methods: ordinary Kriging (OK) and Kriging combined with land use information (LuK). To evaluate the influence of sample discretization on revealing SOC variability, we compared the interpolation accuracies at four discretization levels with uniformly distributed validation points. The results demonstrated that the spatial distribution patterns of SOC were roughly similar, but the contour details in some local areas were different at the various discretization levels. Moreover, the predicted mean absolute errors (MAE) and root mean square errors (RMSE) of the two Kriging methods all rose with an increase in discretization. From the lowest to the largest discretization level, the MAEs of OK and LuK rose from 4.47 and 3.02 g kg−1 to 5.46 and 3.54 g kg−1, and the RMSEs rose from 5.13 and 3.95 g kg−1 to 5.76 and 4.76 g kg−1, respectively. Though the trend of prediction errors varied with discretization levels, the interpolation accuracies of the two Kriging methods were both influenced by the sample discretization level. Furthermore, the spatial interpolation uncertainty of OK was more sensitive to the discretization level than that of the LuK method. Therefore, when the spatial distribution of SOC is predicted using Kriging methods based on the same sample quantity, the more uniformly distributed sampling points are, the more accurate the spatial prediction accuracy of SOC will be, and vice versa. The results of this study can act as a useful reference for evaluating the uncertainty of SOC spatial interpolation and making a soil sampling scheme in the red soil region of China. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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18 pages, 2323 KiB  
Article
Functional Diversity of Soil Microbial Communities in Response to the Application of Cefuroxime and/or Antibiotic-Resistant Pseudomonas putida Strain MC1
by Kamila Orlewska, Anna Markowicz, Zofia Piotrowska-Seget, Joanna Smoleń-Dzirba and Mariusz Cycoń
Sustainability 2018, 10(10), 3549; https://doi.org/10.3390/su10103549 - 03 Oct 2018
Cited by 10 | Viewed by 2922
Abstract
Cefuroxime (XM), the most commonly prescribed antibiotic from the cephalosporin group, may cause changes in the structure of the soil microbial community, and these changes may also be reflected in the alteration of its functionality. Therefore, due to the lack of studies on [...] Read more.
Cefuroxime (XM), the most commonly prescribed antibiotic from the cephalosporin group, may cause changes in the structure of the soil microbial community, and these changes may also be reflected in the alteration of its functionality. Therefore, due to the lack of studies on this topic, the scope of this study was to assess the functional diversity and catabolic activity of the microbial community in soil treated with XM (1 mg/kg and 10 mg/kg soil) using the community-level physiological profile (CLPP) approach during a 90-day experiment. In addition, the effect of antibiotic-resistant Pseudomonas putida strain MC1 (Ps) was also evaluated. The resistance/resilience concept and multifactorial analysis were used to interpret the data. The results showed that the introduction of XM and/or Ps into the soil caused changes in the catabolic activity and functional diversity of the microbial community. A decrease in the values of the CLPP indices (i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon-Wiener (H) and evenness (E) indices and the AWCD values for the six carbon substrate groups) for the XM-treated soil was generally detected up to 30 days. In turn, at the same time, the activity measured in the Ps-inoculated soil was higher compared to the control soil. A stimulatory effect of XM at 10 mg/kg (XM10) and XM10+Ps on the utilization pattern of each substrate group was found at the following sampling times (days 60 and 90). The AWCD values for the utilization of amines, amino acids, carbohydrates, carboxylic acids, miscellaneous compounds and polymers for these treatments were found to be up to 2.3-, 3.1-, 2.3-, 13-, 3.4- and 3.3-fold higher compared to the values for the nontreated control, respectively. The resistance of the CLPP indices and the AWCD values for the carbon substrate groups were categorized as follows: E > H > R > AWCD and amino acids = carbohydrates > polymers > amines > miscellaneous > carboxylic acids, respectively. The results suggest a low initial resistance of the soil microbial community to XM and/or Ps, and despite the short-term negative effect, the balance of the soil ecosystem may be disturbed. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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12 pages, 2113 KiB  
Article
Land Use Types and Geomorphic Settings Reflected in Soil Organic Carbon Distribution at the Scale of Watershed
by Ye Yuan, Xueyi Shi and Zhongqiu Zhao
Sustainability 2018, 10(10), 3490; https://doi.org/10.3390/su10103490 - 29 Sep 2018
Cited by 10 | Viewed by 3111
Abstract
Soil organic carbon (SOC) is vital to soil ecosystem function and it plays a key role in carbon cycling in the terrestrial ecosystem. The spatial pattern of SOC stock (SOCs) is affected by specific geomorphic settings and land-use types at the scale of [...] Read more.
Soil organic carbon (SOC) is vital to soil ecosystem function and it plays a key role in carbon cycling in the terrestrial ecosystem. The spatial pattern of SOC stock (SOCs) is affected by specific geomorphic settings and land-use types at the scale of watershed. Nevertheless, the distribution of SOCs with fluvial landform regimes and land use types was not sufficiently elucidated in the semi-humid riparian ecosystem in north China. In this study, 103 soil plots were sampled and spatial auto-correlation method was adopted to detect the spatial pattern of SOCs in the Changhe watershed that was located at the boundary of the Loess Plateau and the Taihang Mountains. The results showed that SOCs in the Changhe watershed varied from 18.03 Mg ha−1 to 21.51 Mg ha−1 and it was in the order: grassland > forestland > cropland > construction land. SOCs varied with geomorphic settings, among which, the altitude exerted more influence on the distribution of SOCs than the aspect and the slope. In terms of the spatial pattern of SOCs, 17 plots with higher SOCs collectively distributed in the west of the watershed and that with lower SOCs (19 plots) concentrated in the midlands. This indicated that the upland had higher SOCs while the lowland had lower values. Overall, land use type and geomorphic settings (especially the altitude) should be considered when estimating the SOC sequestration in warmer and wetter watershed in north China. With regard to the implications for land use management, reforestation could elevate the SOCs. Moreover, no-tillage and returning crop straw to cultivated soils could be efficient approaches to elevate soil carbon sequestration and soil productivity. Full article
(This article belongs to the Special Issue Sustainability of Microbial Ecosystems: Soil and Aquatic Microbial Diversity)
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