scholarly journals Response of bacterial and fungal communities to high petroleum pollution in different soils

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Polina Galitskaya ◽  
Liliya Biktasheva ◽  
Sergey Blagodatsky ◽  
Svetlana Selivanovskaya

AbstractPetroleum pollution of soils is a major environmental problem. Soil microorganisms can decompose a significant fraction of petroleum hydrocarbons in soil at low concentrations (1–5%). This characteristic can be used for soil remediation after oil pollution. Microbial community dynamics and functions are well studied in cases of moderate petroleum pollution, while cases with heavy soil pollution have received much less attention. We studied bacterial and fungal successions in three different soils with high petroleum contents (6 and 25%) in a laboratory experiment. The proportion of aliphatic and aromatic compounds decreased by 4–7% in samples with 6% pollution after 120 days of incubation but remained unchanged in samples with 25% hydrocarbons. The composition of the microbial community changed significantly in all cases. Oil pollution led to an increase in the relative abundance of bacteria such as Actinobacteria and the candidate TM7 phylum (Saccaribacteria) and to a decrease in that of Bacteroidetes. The gene abundance (number of OTUs) of oil-degrading bacteria (Rhodococcus sp., candidate class TM7-3 representative) became dominant in all soil samples, irrespective of the petroleum pollution level and soil type. The fungal communities in unpolluted soil samples differed more significantly than the bacterial communities. Nonmetric multidimensional scaling revealed that in the polluted soil, successions of fungal communities differed between soils, in contrast to bacterial communities. However, these successions showed similar trends: fungi capable of lignin and cellulose decomposition, e.g., from the genera Fusarium and Mortierella, were dominant during the incubation period.

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Rongrong Li ◽  
Di Jiang ◽  
Mingli Zheng ◽  
Pengjiao Tian ◽  
Menghu Zheng ◽  
...  

Abstract This study was conducted to examine the effects of Lactobacillus plantarum (LP) and sucrose (S) on clostridial community dynamics and correlation between clostridia and other bacteria in alfalfa silage during ensiling. Fresh alfalfa was directly ensiled without (CK) or with additives (LP, S, LP + S) for 7, 14, 28 and 56 days. Clostridial and bacterial communities were evaluated by next-generation sequencing. Severe clostridial fermentation occurred in CK, as evidenced by the high contents of butyric acid, ammonia nitrogen, and clostridia counts, whereas all additives, particularly LP + S, decreased silage pH and restrained clostridial fermentation. Clostridium perfringens and Clostridium butyricum might act as the main initiators of clostridial fermentation, with Clostridium tyrobutyricum functioning as the promoters of fermentation until the end of ensiling. Clostridium tyrobutyricum (33.5 to 98.0%) dominated the clostridial community in CK from 14 to 56 days, whereas it was below 17.7% in LP + S. Clostridium was negatively correlated with the genus Lactobacillus, but positively correlated with the genera Enterococcus, Lactococcus and Leuconostoc. Insufficient acidification promoted the vigorous growth of C. tyrobutyricum of silage in later stages, which was mainly responsible for the clostridial fermentation of alfalfa silage.


2021 ◽  
Vol 11 ◽  
Author(s):  
Yanru Chen ◽  
Kaimin Li ◽  
Ting Liu ◽  
Ruyi Li ◽  
Guiming Fu ◽  
...  

Special-flavor Baijiu is a unique Baijiu in Jiangxi Province, China, whose uniqueness mainly depends on the unique production process of special-flavor Baijiu Daqu. However, the microbial structure and physicochemical indices of different parts of the special-flavor Baijiu Daqu are still unknown. This greatly reduces the actual value of Daqu in the production of special-flavor Baijiu. Therefore, culture-dependent and Illumina MiSeq sequencing methods were used to analyze the microbial structure of special-flavor Baijiu Daqu. The results indicated that there was a complicated microbial diversity in Chinese special-flavor Baijiu Daqu. The predominant bacterial communities were Bacillales, Lactobacillales, and Rhodospirillales, while Saccharomycetales and Eurotiales were the predominant fungal communities. Significant differences in microbial community and distribution were shown between the surface and central parts of Daqu. Acetobacter and Pichia genera were the predominant microorganisms in the surface part of Daqu, whereas Aspergillus, Kroppenstedtia, Oceanobacillus, and Bacillus genera were the predominant microorganisms in the central part of Daqu. Meantime, the different microbial distributions between the surface and central parts of Daqu caused the significant differences in the physicochemical indices. These results can provide an important theoretical basis for improving the brewing process and the quality of special-flavor Baijiu.


2008 ◽  
Vol 33 (1) ◽  
pp. 55-64 ◽  
Author(s):  
Yeti Darmayati ◽  
Shigeaki Harayama ◽  
Atsushi Yamazoe ◽  
Ariani Hatmanti ◽  
Sulistiani ◽  
...  

Jakarta Bay has been known as one of the most polluted marine environment in Indonesia, with no exception by oil. Seribu Islands waters, located in the north of Jakarta Bay may have been impacted by this polluted condition.It’s sometimes also hit by oil spillage from pipe leakage. The purpose of this study is to isolate and identify hydrocarbonoclastic bacteria (oil and Polyaromatic Hydrocarbon degrading bacteria) from Jakarta Bay and Seribu Island waters. The bacteria were isolated from water and sediment/sand. Isolation was prepared by enriched samples in SWP medium with Arabian Light Crude Oil (ALCO). Screening for PAH degrading bacteria has been completed by using sublimation plate method in ONR7a medium and screening for oil degrading bacteria were conducted by using oil plated method with the same medium. Bacteria identifications were done based on l6sRNA gene. The results were analyzed using BLAST and showed that 131 potential hydrocarbonoclastic bacteria have been isolated from Jakarta Bay and Seribu Island waters. Most of them were oil degrading bacteria (41.98%) and the rest were PAH degrading bacteria. Oil pollution level may impact the number of strain of hydrocarbonoclastic bacteria isolated. Among the hydrocarbonoclastic bacteria isolated from Jakarta Bay and Seribu Islands, Alcanivorax, Marinobacter, Achromobacter and Bacillus were common hydrocarbonoclastic genera in Jakarta Bay and its surrounding waters. Alcanivorax spp. is important oil and PAH-degrader found not only in temperate waters, but in tropical waters as well.


2021 ◽  
Vol 12 ◽  
Author(s):  
Jing Zhu ◽  
Xiang Sun ◽  
Qi-Yong Tang ◽  
Zhi-Dong Zhang

Endophytes are essential components of plant microbiota. Studies have shown that environmental factors and seasonal alternation can change the microbial community composition of plants. However, most studies have mainly emphasized the transitive endophyte communities and seasonal alternation but paid less attention to their persistence through multiple seasons. Kalidium schrenkianum is a perennial halophyte growing in an arid habitat with radiation stress (137Cs) in northwest China. In this study, K. schrenkianum growing under different environmental stresses were selected to investigate the dynamics and persistency of endophytic microbial communities amid seasons in a year. The results showed that Gammaproteobacteria and unassigned Actinobacteria were the most dominant bacterial communities, while the most dominant fungal communities were Dothideomycetes, unassigned Fungi, and Sodariomycetes. The bacterial community diversity in roots was higher than that in aerial tissues, and root communities had higher diversity in summer and autumn. In contrast, the fungal community diversity was higher in aerial tissues comparing to roots, and the highest diversity was in spring. Season was a determinant factor in the microbial community composition in the roots but not in the aerial tissues. RaupCrick index suggested that the bacterial communities were mainly shaped by stochastic processes. Our research investigated the community traits and members with temporal persistency. For example, bacterial taxa Afipia, Delftia, Stenotrophomonas, Xanthomonadaceae_B_OTU_211, and fungal taxa Neocamarosporium F_OTU_388, F_OTU_404, F_OTU_445, and unassigned Fungi F_OTU_704, F_OTU_767 showed higher frequencies than predicted in all the four seasons tested with neutral community model. The networks of co-occurrence associations presented in two or more seasons were visualized which suggested potential time-continuous core modules in most communities. In addition, the community dynamics and persistency also showed different patterns by radiation levels. Our findings would enhance our understanding of the microbial community assembly under environmental stress, and be promising to improve the development of integrated concept of core microbiome in future.


2021 ◽  
Vol 12 ◽  
Author(s):  
Chao Ji ◽  
Xiaohui Wang ◽  
Xin Song ◽  
Qisheng Zhou ◽  
Chaohui Li ◽  
...  

Plant growth-promoting bacteria (PGPB) can effectively reduce salt damage in plants. Currently, there are many studies on the effects of PGPB on the microbial community structure of rhizosphere soil under salt stress, but fewer studies on the community structure of endophytic bacteria and fungi. We propose that inoculation of endophytic bacteria into the rhizosphere of plants can significantly affect the microbial community structure of the plant’s above-ground and underground parts, which may be the cause of the plant’s “Induced Systemic Tolerance.” The isolated endophytes were re-inoculated into the rhizosphere under salinity stress. We found that, compared with the control group, inoculation with endophytic Bacillus velezensis JC-K3 not only increased the accumulation of wheat biomass, but also increased the content of soluble sugar and chlorophyll in wheat, and reduced the absorption of Na in wheat shoots and leaves. The abundance of bacterial communities in shoots and leaves increased and the abundance of fungal communities decreased after inoculation with JC-K3. The fungal community richness of wheat rhizosphere soil was significantly increased. The diversity of bacterial communities in shoots and leaves increased, and the richness of fungal communities decreased. JC-K3 strain improved wheat’s biomass accumulation ability, osmotic adjustment ability, and ion selective absorption ability. In addition, JC-K3 significantly altered the diversity and abundance of endophytic and rhizosphere microorganisms in wheat. PGPB can effectively reduce plant salt damage. At present, there are many studies on the effect of PGPB on the microbial community structure in rhizosphere soil under salt stress, but there are few studies on the community structure changes of endophytic bacteria and fungi in plants.


2020 ◽  
Author(s):  
Christina Nikolova ◽  
Umer Zeeshan Ijaz ◽  
Clayton Magill ◽  
Sara Kleindienst ◽  
Samantha B. Joye ◽  
...  

AbstractBackgroundAlthough synthetic dispersants are effective in dispersing crude oil, they can alter the natural microbial response to oil and potentially hinder its biodegradation. Biosurfactants, however, are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. This study investigated the microbial community dynamics, ecological drivers, functional diversity, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52.ResultsWe found the microbial community composition and diversity were markedly different in the rhamnolipid-amended treatment compared to that with Finasol, with key aromatic hydrocarbon-degrading bacteria like Cycloclasticus being suppressed in the Finasol treatment but not in oil-only and rhamnolipid-amended treatments. Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment and Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Vibrio abundance increased substantially in treatments receiving Finasol, suggesting a potentially important role for these organisms in degrading dispersant components. In fact, Finasol was linked with a negative impact on alpha diversity. Deterministic environmental filtering played a dominant role in regulating the community assembly in all treatments but was strongest in the dispersant-amended treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment.ConclusionOverall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants affect the natural marine microbial community, supporting their potential application in oil spills.


2020 ◽  
Vol 71 (3) ◽  
pp. 595-607
Author(s):  
Yonggang Wang ◽  
Shengcai Dou ◽  
Qingfang Zhang ◽  
Abdolghaffar Ebadi ◽  
Jixiang Chen ◽  
...  

The problem of environmental pollution caused by the development and use of petroleum is increasingly obvious, which is a serious threat to human health. The use of microbial degradation to treat oil pollution is one of the environmentally effective, economical and practical methods.In order to explore the soil microbial diversity in the desert area of Northwest China, this paper analyzes the soil bacterial diversity of soil samples collected from different oil-contaminated areas in Yumen Oilfield for the oil pollution problem in the Yumen Oilfield in the northwest desert area, and selects the high efficiency through pure culture technology. Petroleum degradation bacteria, and research on the biological characteristics of degrading bacteria. The composition, abundance and diversity of bacterial communities in oil-contaminated soil in Yumen Oilfield were analyzed. The culturable bacteria in western oil-contaminated desert soil were separated by coating plate method. The bacterial morphology and 16S rRNA gene system development analysis were studied. The structure and diversity of bacterial community could be cultured, and the oil utilization and degradation ability of the strain could be analyzed. The microbial diversity of Yumen oil-contaminated desert soil was analyzed by Illumina Miseq high-throughput sequencing. Through research, it is found that there are abundant bacterial groups in the oil-contaminated desert soil, and there are obvious diversity. The genetic material in the variable regions of the six soil samples detected a total of 3943 0TU at 97% similarity level, and obtained the soil microbial community. Doors, 48 classes, 78 orders, 179 families and 471 genera, including most common high-efficiency petroleum-degrading bacteria. Petroleum hydrocarbon pollution can change the microbial diversity and community structure of the original soil. The size of microbial diversity in the six soil samples is B2]A1]B1]A2]C1]C2, the diversity of B2 is the highest, the diversity of C2 is the lowest, and the microbial diversity differed greatly between groups, and there was no difference in the group. Among the dominant bacteria isolated from contaminated soil, 8 strains of oil have a degradation rate of more than 30%, including the species of the genus Rhodococcus and Pseudomonas. Soil desertification in western China has a great impact on the local ecological environment. Studying the microbial diversity of desert soils and separating high-efficiency petroleum-degrading strains is of great significance for strengthening the ecological restoration of oil-contaminated environment in desert areas.


Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Christina N. Nikolova ◽  
Umer Zeeshan Ijaz ◽  
Clayton Magill ◽  
Sara Kleindienst ◽  
Samantha B. Joye ◽  
...  

Abstract Background Biosurfactants are naturally derived products that play a similar role to synthetic dispersants in oil spill response but are easily biodegradable and less toxic. Using a combination of analytical chemistry, 16S rRNA amplicon sequencing and simulation-based approaches, this study investigated the microbial community dynamics, ecological drivers, functional diversity and robustness, and oil biodegradation potential of a northeast Atlantic marine microbial community to crude oil when exposed to rhamnolipid or synthetic dispersant Finasol OSR52. Results Psychrophilic Colwellia and Oleispira dominated the community in both the rhamnolipid and Finasol OSR52 treatments initially but later community structure across treatments diverged significantly: Rhodobacteraceae and Vibrio dominated the Finasol-amended treatment, whereas Colwellia, Oleispira, and later Cycloclasticus and Alcanivorax, dominated the rhamnolipid-amended treatment. Key aromatic hydrocarbon-degrading bacteria, like Cycloclasticus, was not observed in the Finasol treatment but it was abundant in the oil-only and rhamnolipid-amended treatments. Overall, Finasol had a significant negative impact on the community diversity, weakened the taxa-functional robustness of the community, and caused a stronger environmental filtering, more so than oil-only and rhamnolipid-amended oil treatments. Rhamnolipid-amended and oil-only treatments had the highest functional diversity, however, the overall oil biodegradation was greater in the Finasol treatment, but aromatic biodegradation was highest in the rhamnolipid treatment. Conclusion Overall, the natural marine microbial community in the northeast Atlantic responded differently to crude oil dispersed with either synthetic or biogenic surfactants over time, but oil degradation was more enhanced by the synthetic dispersant. Collectively, our results advance the understanding of how rhamnolipid biosurfactants and synthetic dispersant Finasol affect the natural marine microbial community in the FSC, supporting their potential application in oil spills.


2017 ◽  
Vol 1 (1) ◽  
pp. 24-35 ◽  
Author(s):  
Matthew G. Bakker ◽  
Thomas B. Moorman ◽  
Thomas C. Kaspar ◽  
Daniel K. Manter

The dynamics of microbial communities associated with dying cover crops are of interest because of potential impacts on disease in a subsequent crop, and because of the importance of microbial activity on plant residue to soil organic matter dynamics and nutrient cycling. We used high throughput amplicon sequencing to characterize the composition and structure of oomycete and fungal communities associated with a rye cover crop, and to track their community dynamics in the first several weeks after herbicide was applied to terminate the cover crop. The dominant oomycetes associated with cereal rye roots were Pythium volutum, Pythium sp. F86 (an unknown species within clade B), and Lagena radicicola. Because P. volutum is sensitive to common additives in isolation media, and L. radicicola is an obligate intracellular parasite, a unique aspect of this work is to reveal the dominance of oomycete taxa that would have been missed entirely under a traditional cultivation-based approach. Based on first detection in an amplicon sequencing survey, we were able to isolate P. volutum and Pythium sp. F86. We demonstrate that both species are pathogenic on corn, and that corn seedlings grown in the field following a rye cover crop show elevated rates of infection by P. volutum, highlighting a potential disease risk associated with cover cropping. P. volutum and Pythium sp. F86 exhibited contrasting spatial patterns of abundance, with nearly complete turnover of the dominant species across the field site. In contrast to the strong spatial structuring and low diversity of oomycete communities, fungal communities associated with a cereal rye cover crop were more diverse and dynamic, with some displacement of basidiomycetes by ascomycetes over time. Several plant pathogens, as well as putative beneficial organisms, were detected among fungal communities associated with rye roots. This work sheds light on microbial community dynamics on dying host plants, highlights the power of culture-independent microbial community assessment to yield new insights, and suggests the need for informed management to reduce seedling disease risk in corn following rye cover crops.


Author(s):  
Nan Xiang ◽  
Christiane Hassenrück ◽  
Claudia Pogoreutz ◽  
Nils Rädecker ◽  
Susana Marcela Simancas-Giraldo ◽  
...  

Mutualistic nutrient cycling in the coral-algae symbiosis depends on limited nitrogen (N) availability for algal symbionts. Denitrifying prokaryotes capable of reducing nitrate or nitrite to dinitrogen could thus support coral holobiont functioning by limiting N availability. Octocorals show some of the highest denitrification rates among reef organisms, however little is known about the community structures of associated denitrifiers and their response to environmental fluctuations. Combining 16S rRNA gene amplicon sequencing with nirS in-silico PCR and quantitative PCR, we found differences in bacterial community dynamics between two octocorals exposed to excess dissolved organic carbon (DOC) and concomitant warming. While bacterial communities of the gorgonian Pinnigorgia flava remained largely unaffected by DOC and warming, the soft coral Xenia umbellata exhibited a pronounced shift towards Alphaproteobacteria dominance under excess DOC. Likewise, the relative abundance of denitrifiers was not altered in P. flava , but decreased by one order of magnitude in X. umbellata under excess DOC likely due to decreased proportions of Ruegeria spp. Given that holobiont C:N ratios remained stable in P. flava but showed a pronounced increase with excess DOC in X. umbellata host, our results suggest that microbial community dynamics may reflect the nutritional status of the holobiont. Hence, denitrifier abundance may be directly linked to N availability. This suggests a passive regulation of N cycling microbes, which could help stabilize nutrient limitation in the coral-algal symbiosis and thereby support holobiont functioning in a changing environment. Importance Octocorals are important members of reef-associated benthic communities that can rapidly replace scleractinian corals as the dominant ecosystem engineers on degraded reefs. Considering the substantial change in the (a)biotic environment that is commonly driving reef degradation, maintaining a dynamic and metabolically diverse microbial community might contribute to octocoral acclimatization and ecological adaptation. Nitrogen (N) cycling microbes, in particular denitrifying prokaryotes, may support holobiont functioning by limiting internal N availability, but little is known about the identity and (a)biotic drivers of octocoral-associated denitrifiers. Here, we show contrasting dynamics of bacterial communities associated with two common octocoral species, the soft coral Xenia umbellata and the gorgonian Pinnigorgia flava after a six-week exposure to excess dissolved organic carbon (DOC) under concomitant warming conditions. The specific responses of denitrifier communities associated with the two octocoral species aligned with the nutritional status of holobiont members. This suggests a passive regulation of this microbial trait based on N availability in the coral holobiont.


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