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Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone

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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 December 2021) | Viewed by 31452

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Special Issue Editors

Dr. Tsing Bohu

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Guest Editor

1. CSIRO Mineral Resources, Australian Resources and Research Centre, Kensington, WA 6151, Australia
2. State Key Laboratory of Lunar and Planetary Sciences, Macau University of Science and Technology, Taipa, Macau
Interests: biogeochemistry; Critical Zone; geomicrobiology; metals and microbes
Special Issues, Collections and Topics in MDPI journals

Prof. Dr. Xuliang Zhuang

E-Mail Website
Co-Guest Editor

Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
Interests: nitrogen cycle; microbial ecology; constructed wetlands; watershed management; wastewater treatment; aquatic ecology; wastewater reuse and resource recovery; quorum sensing; partial nitrification
Special Issues, Collections and Topics in MDPI journals

Dr. Ignacio Gonzalez-Alvarez

E-Mail Website
Co-Guest Editor

CSIRO, 26 Dick Perry Ave., Kensington, WA 6151, Australia
Interests: sedimentary geochemistry; deep weathering; landscape evolution; mineral exploration; hydrothermal systems

Special Issue Information

Dear Colleagues,

From the top of vegetation canopies to the topmost zones of groundwater, the Critical Zone (CZ) is the Earth's outer shell where all fundamental physical, chemical, and biological processes that are critical for sustaining life occur and interact. Processes such as secondary ore precipitation, sediment formation, rock weathering, soil bleaching, streamflow generation, and supergene biogeochemical cycling within the critical zone support many ecosystem processes and, consequently, provide a variety of products and services to humans. Element transportation and transformation in the CZ is a series of essential processes, and microorganisms are deemed one of the drivers for these interactions.

The Special Issue aims to provide an adequate multidisciplinary platform for the interchange of constructive information (both basic and applied research) that aids in the understanding of microbe-driven migration and transformation of elements in the surface and subsurface environments. The collection of information can also be used to establish links and integrate element cycles to the composition and functions of autochthonous geology, environmental chemistry, and the indigenous microbiota.

As Guest Editor, I invite researchers to submit research articles, review articles, and short communications related to microbe-drive migration and transformation of elements through the Earth’s Critical Zone for inclusion in this Special Issue.

Dr. Tsing Bohu
Guest Editor
Prof. Dr. Xuliang Zhuang
Dr. Ignacio Gonzalez-Alvarez
Co-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.

Keywords

Critical Zone
biogeochemical cycling of elements
transportation and transformation of elements
environmental remediation
landscape evolution
microbial communities
mineral exploration
rhizosphere
regolith and sedimentary

Published Papers (12 papers)

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Research

13 pages, 1375 KiB

Open AccessArticle

Interactions of Vallisneria natans and Iron-Oxidizing Bacteria Enhance Iron-Bound Phosphorus Formation in Eutrophic Lake Sediments

by Juanjuan Wang, Mingming Gao, Yanju Yang, Shipeng Lu, Guiliang Wang and Xiaoqing Qian

Microorganisms 2022, 10(2), 413; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020413 - 11 Feb 2022

Cited by 3 | Viewed by 1597

Abstract

Submerged macrophyte restoration and in situ phosphorus (P) passivation are effective methods for the control of internal P loading from sediments. This study explored the synergistic effects of Vallisneria natans and iron (Fe)-oxidizing bacteria (IOB) on internal P loading from eutrophic freshwater lake sediments by taking into account Fe-bound P (FeP) formation and associated bacterial community structures. Sediment samples were prepared in glass tanks under four treatments, namely no V. natans planting or IOB inoculation (control), planting V. natans without IOB inoculation (Va), planting V. natans with IOB inoculation (Va-IOB), and planting V. natans with autoclaved IOB inoculation (Va-IOB[A]). Compared with the control, all three treatments with V. natans (Va, Va-IOB, and Va-IOB[A]) had significantly decreased organic matter contents and increased redox potential in sediments (p < 0.05), at the rapid growth and mature stages of V. natans. Planting V. natans with and without IOB inoculation also decreased the total P (TP) and Fe–P concentrations in sediments. Conversely, Fe³⁺ concentrations, Fe³⁺/Fe²⁺ ratios, and the proportions of Fe–P in TP all increased in sediments planted with V. natans, especially under the Va-IOB treatment (p < 0.05). Furthermore, bacterial community diversity increased in sediments due to the presence of V. natans. The relative abundances of IOB (including Acidovorax and Chlorobium) increased from the transplanting to the rapid growth stage of V. natans and then decreased afterwards. In the later stages, the relative abundances of IOB and their ratios to Fe-reducing bacteria were the highest under the Va-IOB treatment. Accordingly, synergistic interactions between V. natans and IOB could enhance Fe–P formation and reduce TP concentrations in eutrophic lake sediments by altering sediment physicochemical properties and Fe oxidation-related bacterial community structures. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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7 pages, 2187 KiB

Open AccessCommunication

The Immediate Hotspot of Microbial Nitrogen Cycling in an Oil-Seed Rape (Brassica campestris L.) Soil System Is the Bulk Soil Rather Than the Rhizosphere after Biofertilization

by Shanghua Wu, Tsing Bohu, Yuzhu Dong, Shijie Wang, Shijie Zhao, Haonan Fan and Xuliang Zhuang

Microorganisms 2022, 10(2), 247; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10020247 - 23 Jan 2022

Cited by 2 | Viewed by 2356

Abstract

Biofertilizers are substances that promote plant growth through the efficacy of living microorganisms. The functional microbes comprising biofertilizers are effective mediators in plant-soil systems in the regulation of nitrogen cycling, especially in nitrification repression. However, the deterministic or stochastic distribution of the functional hotspot where microbes are active immediately after biofertilization is rarely investigated. Here, pot experiments with oil-seed rape (Brassica campestris L.) were conducted with various chemical and biological fertilizers in order to reveal the distribution of the hotspot after each fertilization. A stimulated dynamic of the nitrogen cycling-related genes in the bulk soil inferred that the bulk soil was likely to be the hotspot where the inoculated bacterial fertilizers dominated the nitrogen cycle. Furthermore, a network analysis showed that bulk soil microbial communities were more cooperative than those in the rhizosphere after biofertilization, suggesting that the microbiome of the bulk soils were more efficient for nutrient cycling. In addition, the relatively abundant ammonia-oxidizing bacteria and archaea present in the networks of bulk soil microbial communities further indicated that the bulk soil was the plausible hotspot after the application of the biofertilizers. Therefore, our research provides a new insight into the explicit practice of plant fertilization and agricultural management, which may improve the implementational efficiency of biofertilization. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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23 pages, 4605 KiB

Open AccessArticle

From Surface to Subsurface: Diversity, Composition, and Abundance of Sessile and Endolithic Bacterial, Archaeal, and Eukaryotic Communities in Sand, Clay and Rock Substrates in the Laurentians (Quebec, Canada)

by Julia Meyer, Sheri Zakhary, Marie Larocque and Cassandre S. Lazar

Microorganisms 2022, 10(1), 129; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010129 - 08 Jan 2022

Cited by 6 | Viewed by 2330

Abstract

Microbial communities play an important role in shallow terrestrial subsurface ecosystems. Most studies of this habitat have focused on planktonic communities that are found in the groundwater of aquifer systems and only target specific microbial groups. Therefore, a systematic understanding of the processes that govern the assembly of endolithic and sessile communities is still missing. This study aims to understand the effect of depth and biotic factors on these communities, to better unravel their origins and to compare their composition with the communities detected in groundwater. To do so, we collected samples from two profiles (~0–50 m) in aquifer sites in the Laurentians (Quebec, Canada), performed DNA extractions and Illumina sequencing. The results suggest that changes in geological material characteristics with depth represent a strong ecological and phylogenetical filter for most archaeal and bacterial communities. Additionally, the vertical movement of water from the surface plays a major role in shallow subsurface microbial assembly processes. Furthermore, biotic interactions between bacteria and eukaryotes were mostly positive which may indicate cooperative or mutualistic potential associations, such as cross-feeding and/or syntrophic relationships in the terrestrial subsurface. Our results also point toward the importance of sampling both the geological formation and groundwater when it comes to studying its overall microbiology. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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15 pages, 1620 KiB

Open AccessArticle

Examining the Osmotic Response of Acidihalobacter aeolianus after Exposure to Salt Stress

by Melissa K. Corbett, Liam Anstiss, April Gifford, Ross M. Graham and Elizabeth L. J. Watkin

Microorganisms 2022, 10(1), 22; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms10010022 - 23 Dec 2021

Cited by 2 | Viewed by 2112

Abstract

Acidihalobacter aeolianus is an acidophilic, halo-tolerant organism isolated from a marine environment near a hydrothermal vent, an ecosystem whereby levels of salinity and total dissolved salts are constantly fluctuating creating ongoing cellular stresses. In order to survive these continuing changes, the synthesis of compatible solutes—also known as organic osmolytes—is suspected to occur, aiding in minimising the overall impact of environmental instability. Previous studies on A. aeolianus identified genes necessary for the accumulation of proline, betaine and ectoine, which are known to act as compatible solutes in other halophilic species. In this study, the impact of increasing the osmotic stress as well as the toxic ion effect was investigated by subjecting A. aeolianus to concentrations of NaCl and MgSO₄ up to 1.27 M. Exposure to high concentrations of Cl⁻ resulted in the increase of ectC expression in log-phase cells with a corresponding accumulation of ectoine at stationary phase. Osmotic stress via MgSO₄ exposure did not trigger the same up-regulation of ectC or accumulation of ectoine, indicating the transcriptionally regulated response against osmotic stress was induced by chloride toxicity. These findings have highlighted how the adaptive properties of halo-tolerant organisms in acidic environments are likely to differ and are dependent on the initial stressor. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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16 pages, 4851 KiB

Open AccessArticle

Assessment of Carbon Substrate Catabolism Pattern and Functional Metabolic Pathway for Microbiota of Limestone Caves

by Suprokash Koner, Jung-Sheng Chen, Bing-Mu Hsu, Chao-Wen Tan, Cheng-Wei Fan, Tsung-Hsien Chen, Bashir Hussain and Viji Nagarajan

Microorganisms 2021, 9(8), 1789; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081789 - 23 Aug 2021

Cited by 21 | Viewed by 3718

Abstract

Carbon utilization of bacterial communities is a key factor of the biomineralization process in limestone-rich curst areas. An efficient carbon catabolism of the microbial community is associated with the availability of carbon sources in such an ecological niche. As cave environments promote oligotrophic (carbon source stress) situations, the present study investigated the variations of different carbon substrate utilization patterns of soil and rock microbial communities between outside and inside cave environments in limestone-rich crust topography by Biolog EcoPlate™ assay and categorized their taxonomical structure and predicted functional metabolic pathways based on 16S rRNA amplicon sequencing. Community level physiological profiling (CLPP) analysis by Biolog EcoPlate™ assay revealed that microbes from outside of the cave were metabolically active and had higher carbon source utilization rate than the microbial community inside the cave. 16S rRNA amplicon sequence analysis demonstrated, among eight predominant bacterial phylum Planctomycetes, Proteobacteria, Cyanobacteria, and Nitrospirae were predominantly associated with outside-cave samples, whereas Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes were associated with inside-cave samples. Functional prediction showed bacterial communities both inside and outside of the cave were functionally involved in the metabolism of carbohydrates, amino acids, lipids, xenobiotic compounds, energy metabolism, and environmental information processing. However, the amino acid and carbohydrate metabolic pathways were predominantly linked to the outside-cave samples, while xenobiotic compounds, lipids, other amino acids, and energy metabolism were associated with inside-cave samples. Overall, a positive correlation was observed between Biolog EcoPlate™ assay carbon utilization and the abundance of functional metabolic pathways in this study. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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19 pages, 20974 KiB

Open AccessArticle

The Impact of Ecological Restoration on Biogeochemical Cycling and Mercury Mobilization in Anoxic Conditions on Former Mining Sites in French Guiana

by Ewan Couic, Alicia Tribondeau, Vanessa Alphonse, Alexandre Livet, Michel Grimaldi and Noureddine Bousserrhine

Microorganisms 2021, 9(8), 1702; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081702 - 10 Aug 2021

Cited by 1 | Viewed by 2275

Abstract

Successive years of gold mining in French Guiana has resulted in soil degradation and deforestation leading to the pollution and erosion of mining plots. Due to erosion and topography, gold panning sites are submitted to hydromorphy during rainfall and groundwater increases. This original study focused on characterizing the impact of hydromorphic anaerobic periods on bio-geochemical cycles. We sampled soil from five rehabilitated sites in French Guiana, including sites with herbaceous vegetation and sites restored with fabaceous plants, Clitoria racemosa (Cli) mon-oculture, Acacia mangium (Aca) monoculture, Clitoria racemosa and Acacia mangium (Mix) bi-culture. We conducted mesocosm experiments where soil samples were incubated in anaerobic conditions for 35 days. To evaluate the effect of anaerobic conditions on biogeochemical cycles, we measured the following parameters related to iron-reducing bacteria and sulfate-reducing bacteria metabolism throughout the experiment: CO₂ release, carbon dissolution, sulphide production and sulphate mobilization. We also monitored the solubilization of iron oxyhydroxides, manganese oxides, aluminum oxides and mercury in the culture medium. Iron-reducing bacteria (IRB) and sulfate-reducing bacteria (SRB) are described as the major players in the dynamics of iron, sulfur and metal elements including mercury in tropical environments. The results revealed two trends in these rehabilitated sites. In the Aca and Mix sites, bacterial iron-reducing activity coupled with manganese solubilization was detected with no mercury solubilization. In herbaceous sites, a low anaerobic activity coupled with sulphide production and mercury solubilization were detected. These results are the first that report the presence and activity of iron- and sulfate-reductive communities at rehabilitated mining sites and their interactions with the dynamics of metallic elements and mercury. These results report, however, the positive impact of ecological restoration of mining sites in French Guiana by reducing IRB and SRB activities, the potential mobility of mercury and its risk of transfer and methylation. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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35 pages, 16323 KiB

Open AccessArticle

Preservation of Underground Microbial Diversity in Ancient Subsurface Deposits (>6 Ma) of the Rio Tinto Basement

by David C. Fernández-Remolar, David Gómez-Ortiz, Per Malmberg, Ting Huang, Yan Shen, Angélica Anglés and Ricardo Amils

Microorganisms 2021, 9(8), 1592; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9081592 - 27 Jul 2021

Cited by 5 | Viewed by 2965

Abstract

The drilling of the Rio Tinto basement has provided evidence of an underground microbial community primarily sustained by the Fe and S metabolism through the biooxidation of pyrite orebodies. Although the gossan is the microbial activity product, which dates back to the Oligocene (25 Ma), no molecular evidence of such activity in the past has been reported yet. A Time of Flight Secondary Ion Mass Spectrometry (ToF-SIMS) molecular analysis of a subsurface sample in the Peña de Hierro basement has provided novel data of the ancient underground microbial community. It shows that the microbial remains are preserved in a mineral matrix composed of laminated Fe-oxysulfates and K- and Na-bearing sulfates alternating with secondary silica. In such a mineral substrate, the biomolecule traces are found in five different microstructure associations, (1) <15 micron-sized nodular microstructures composed of PO_n(2≤n≤4)⁻, (2) <30 micron-size micronodules containing fatty acids, acylglycerides, and alkanol chains, (3) <20 micro-sized nodules containing NO_n⁻_(2≤n≤3) ions, (4) 40-micron size nodules with NH₄⁺ and traces of peptides, and (5) >200-micron thick layer with N-bearing adducts, and sphingolipid and/or peptide traces. It suggests the mineralization of at least five microbial preserved entities with different metabolic capabilities, including: (1) Acidiphilium/Tessaracoccus-like phosphate mineralizers, (2) microbial patches preserving phosphate-free acylglycerides bacteria, (3) nitrogen oxidizing bacteria (e.g., Acidovorax sp.), (4) traces of heterotrophic ammonifying bacteria, and (5) sphingolipid bearing bacteria (e.g., Sphingomonadales, and δ-Proteobacteria) and/or mineralized biofilms. The primary biooxidation process acted as a preservation mechanism to release the inorganic ions that ultimately mineralized the microbial structures. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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17 pages, 2038 KiB

Open AccessArticle

Straw Incorporation with Nitrogen Amendment Shapes Bacterial Community Structure in an Iron-Rich Paddy Soil by Altering Nitrogen Reserves

by Juanjuan Wang, Yao Ma, Lin Di, Xiaoqing Qian and Guiliang Wang

Microorganisms 2021, 9(5), 988; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9050988 - 03 May 2021

Cited by 9 | Viewed by 2161

Abstract

Incorporation of crop straw into the soil along with inorganic fertilization is a widespread agricultural practice and is essential in nutrient-scarce soils, such as iron-rich (ferruginous) paddy soils. The responses of soil bacterial communities to straw incorporation under different nitrogen inputs in iron-rich soils remain unclear. Therefore, 6000 kg ha⁻¹ dry wheat (Triticum aestivum L. cv. Zhengmai 12) straw was applied to a rice paddy with and without nitrogen amendment (0, 80, 300, and 450 kg ha⁻¹ N as urea), to investigate its effects on soil fertility and bacterial community structure. Organic matter, total nitrogen, and water contents tended to decrease in straw-incorporated soils with different nitrogen inputs. Proteobacteria was the dominant bacterial phylum across all treatments (26.3–32.5% of total sequences), followed by Chloroflexi, Acidobacteria, and Nitrospirae. Up to 18.0% of all the taxa in the bacterial communities were associated with iron cycling. Straw incorporation with nitrogen amendment increased the relative abundance of iron oxidizers, Gallionellaceae, while decreasing the relative abundance of iron reducers, Geobacteraceae. Bacterial community composition shifted in different treatments, with total nitrogen, water, and Fe(III) contents being the key drivers. Straw incorporation supplemented by 300 kg ha⁻¹ N increased bacterial richness and enhanced all the predicted bacterial functions, so that it is recommended as the optimal nitrogen dosage in practice. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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15 pages, 10674 KiB

Open AccessArticle

Influence of Temperature and Sulfate Concentration on the Sulfate/Sulfite Reduction Prokaryotic Communities in the Tibetan Hot Springs

by Li Ma, Weiyu She, Geng Wu, Jian Yang, Dorji Phurbu and Hongchen Jiang

Microorganisms 2021, 9(3), 583; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9030583 - 12 Mar 2021

Cited by 8 | Viewed by 1997

Abstract

The distribution and diversity of sulfate/sulfite reduction prokaryotic (SRP) communities in hot springs from the Quzhuomu and Daggyai Geothermal Zone of Tibetan, China, was reported for the first time. In hot springs that are naturally hyperthermal and anoxic, the sulfur cycle is one of the most active cycles of the elements. The distribution of SRP in response to temperature is of great importance to the understanding of biogeochemical cycling of sulfur in geothermal features. Little is known about the SRP in geothermal zone. In this study, the diversity of SRP was investigated in the sediments from the Daggyai and Quzhuomu geothermal zone using PCR amplification, cloning and sequencing of the dissimilatory sulfite reductase beta subunit gene (dsrB). The abundance of dsrB and 16S rRNA genes, were determined by quantitative polymerase chain reactions. In addition, correlations of the SRP assemblages with environmental factors were analyzed by the aggregated boosted tree (ABT) statistical analysis. The results showed that SRP populations were diverse, but were mainly composed of Desulfobacterales, Desulfovibrionales, Syntrophobacterales, Clostridia and Nitrospirales, and large fraction (25%) of novel sequences have branched groups in the dsrB phylogenetic tree. In Quzhuomu geothermal zone, sulfate-rich hot springs are characterized by thick bacterial mats that are green or red and the SRP populations mainly appear at mid-temperature (50 °C to 70 °C). In low-sulfate hot springs in the Daggyai geothermal zone, although gray or pink streamers are widely formed at 60 °C to 80 °C, they prefer to inhabit in green mat at lower temperature (30 °C to 50 °C). With increasing temperature, the diversity of the dsrB gene at the OTU level (cutoff 97%) decreased, while its relative abundance increased. This result suggests that temperature played an important role in affecting dsrB gene distribution. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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19 pages, 2655 KiB

Open AccessArticle

Mineralosphere Microbiome Leading to Changed Geochemical Properties of Sedimentary Rocks from Aiqigou Mud Volcano, Northwest China

by Ke Ma, Anzhou Ma, Guodong Zheng, Ge Ren, Fei Xie, Hanchang Zhou, Jun Yin, Yu Liang, Xuliang Zhuang and Guoqiang Zhuang

Microorganisms 2021, 9(3), 560; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9030560 - 09 Mar 2021

Cited by 3 | Viewed by 1918

Abstract

The properties of rocks can be greatly affected by seepage hydrocarbons in petroleum-related mud volcanoes. Among them, the color of sedimentary rocks can reflect the changes of sedimentary environment and weathering history. However, little is known about the microbial communities and their biogeochemical significance in these environments. In this study, contrasting rock samples were collected from the Aiqigou mud volcano on the southern margin of the Junggar Basin in Northwest China as guided by rock colors indicative of redox conditions. The physicochemical properties and mineral composition are similar under the same redox conditions. For example, the content of chlorite, muscovite, quartz, and total carbon were higher, and the total iron was lower under reduced conditions compared with oxidized environments. High-throughput sequencing of 16S rRNA gene amplicons revealed that different functional microorganisms may exist under different redox conditions; microbes in oxidized conditions have higher diversity. Statistical analysis and incubation experiments indicated that the microbial community structure is closely related to the content of iron which may be an important factor for color stratification of continental sedimentary rocks in the Aiqigou mud volcano. The interactions between organics and iron-bearing minerals mediated by microorganisms have also been hypothesized. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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29 pages, 24218 KiB

Open AccessArticle

Disentangling Responses of the Subsurface Microbiome to Wetland Status and Implications for Indicating Ecosystem Functions

by Jie Gao, Miao Liu, Sixue Shi, Ying Liu, Yu Duan, Xianguo Lv, Tsing Bohu, Yuehui Li, Yuanman Hu, Na Wang, Qiuying Wang, Guoqiang Zhuang and Xuliang Zhuang

Microorganisms 2021, 9(2), 211; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9020211 - 20 Jan 2021

Cited by 6 | Viewed by 2971

Abstract

In this study, we analyzed microbial community composition and the functional capacities of degraded sites and restored/natural sites in two typical wetlands of Northeast China—the Phragmites marsh and the Carex marsh, respectively. The degradation of these wetlands, caused by grazing or land drainage for irrigation, alters microbial community components and functional structures, in addition to changing the aboveground vegetation and soil geochemical properties. Bacterial and fungal diversity at the degraded sites were significantly lower than those at restored/natural sites, indicating that soil microbial groups were sensitive to disturbances in wetland ecosystems. Further, a combined analysis using high-throughput sequencing and GeoChip arrays showed that the abundance of carbon fixation and degradation, and ~95% genes involved in nitrogen cycling were increased in abundance at grazed Phragmites sites, likely due to the stimulating impact of urine and dung deposition. In contrast, the abundance of genes involved in methane cycling was significantly increased in restored wetlands. Particularly, we found that microbial composition and activity gradually shifts according to the hierarchical marsh sites. Altogether, this study demonstrated that microbial communities as a whole could respond to wetland changes and revealed the functional potential of microbes in regulating biogeochemical cycles. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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20 pages, 2669 KiB

Open AccessArticle

Unraveling Mechanisms and Impact of Microbial Recruitment on Oilseed Rape (Brassica napus L.) and the Rhizosphere Mediated by Plant Growth-Promoting Rhizobacteria

by Ying Liu, Jie Gao, Zhihui Bai, Shanghua Wu, Xianglong Li, Na Wang, Xiongfeng Du, Haonan Fan, Guoqiang Zhuang, Tsing Bohu and Xuliang Zhuang

Microorganisms 2021, 9(1), 161; https://0-doi-org.brum.beds.ac.uk/10.3390/microorganisms9010161 - 12 Jan 2021

Cited by 32 | Viewed by 3385

Abstract

Plant growth-promoting rhizobacteria (PGPR) are noticeably applied to enhance plant nutrient acquisition and improve plant growth and health. However, limited information is available on the compositional dynamics of rhizobacteria communities with PGPR inoculation. In this study, we investigated the effects of three PGPR strains, Stenotrophomonas rhizophila, Rhodobacter sphaeroides, and Bacillus amyloliquefaciens on the ecophysiological properties of Oilseed rape (Brassica napus L.), rhizosphere, and bulk soil; moreover, we assessed rhizobacterial community composition using high-throughput Illumina sequencing of 16S rRNA genes. Inoculation with S. rhizophila, R. sphaeroides, and B. amyloliquefaciens, significantly increased the plant total N (TN) (p < 0.01) content. R. sphaeroides and B. amyloliquefaciens selectively enhanced the growth of Pseudomonadacea and Flavobacteriaceae, whereas S. rhizophila could recruit diazotrophic rhizobacteria, members of Cyanobacteria and Actinobacteria, whose abundance was positively correlated with inoculation, and improved the transformation of organic nitrogen into inorganic nitrogen through the promotion of ammonification. Initial colonization by PGPR in the rhizosphere affected the rhizobacterial community composition throughout the plant life cycle. Network analysis indicated that PGPR had species-dependent effects on niche competition in the rhizosphere. These results provide a better understanding of PGPR-plant-rhizobacteria interactions, which is necessary to develop the application of PGPR. Full article

(This article belongs to the Special Issue Microbe-Driven Migration and Transformation of Elements through the Earth’s Critical Zone)

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