Bacterial succession in a petroleum land treatment unit

Composition and assembly mechanisms of prokaryotic communities in wetlands, and their relationships with different vegetation and reclamation methods

Coastal wetlands are undergoing substantial transformations globally as a result of increased human activities. However, compared to other ecosystems, diversity and functional characteristics of microbial communities in reclaimed coastal wetlands are not well studied compared to other ecosystems. This is important because it is known that microorganisms can play a crucial role in biogeochemical cycling within coastal wetland ecosystems. Hence, this study utilized the high-throughput sequencing technique to investigate the structure and assembly processes of microbial communities in reclaimed coastal wetlands. The results revealed a substantial change in soil properties following coastal wetland reclamation. Remarkably, the reclaimed soil exhibited significantly lower pH, soil organic carbon (SOC), and total salinity (TS) values (p < 0.05). The dominant phyla included Proteobacteria, Chloroflexi, Bacteroidetes, Acidobacteria, and Planctomycetes among study sites. However, the relative abundance of Proteobacteria increased from un-reclaimed coastal wetlands to reclaimed ones. The Proteobacteria, Chloroflexi, and Acidobacteria showed higher relative abundance in vegetated soil compared to bare soil, while Bacteroidetes and Planctomycetes exhibited the opposite trend. Notably, vegetation types exerted the strongest influence on microbial diversity, surpassing the effects of soil types and depth (F = 34.49, p < 0.001; F = 25.49, p < 0.001; F = 3.173, p < 0.078, respectively). Stochastic assembly processes dominated in un-reclaimed soil, whereas deterministic processes governed the assembly in artificial sea embankment wetlands (SEW). The presence of Spartina alterniflora in all soil types (except SEW soils) indicated stochastic assembly, while Phragmites australis in reclaimed soils pointed toward deterministic microbial assembly. Furthermore, environmental factors such as pH, soil water content (SWC), SOC, total carbon (TC), total nitrogen (TN), total phosphorus (TP), NH4+-N, vegetation types, soil depth, and geographic distance exhibited significant effects on microbial beta diversity indices. Co-occurrence network analysis revealed a stronger association between taxa in SEW compared to land reclaimed from wetlands (LRW) and natural coastal wetlands (NCW). The bottom soil layer exhibited more complex network interactions than the topsoil layer. Besides soil parameters, reclamation and varieties of vegetation were also substantial factors influencing the composition, diversity, and assembly processes of microbial communities in coastal wetlands.

Microbial remediation of oil-contaminated shorelines: a review

Frequent marine oil spills have led to increasingly serious oil pollution along shorelines. Microbial remediation has become a research hotspot of intertidal oil pollution remediation because of its high efficiency, low cost, environmental friendliness, and simple operation. Many microorganisms are able to convert oil pollutants into non-toxic substances through their growth and metabolism. Microorganisms use enzymes' catalytic activities to degrade oil pollutants. However, microbial remediation efficiency is affected by the properties of the oil pollutants, microbial community, and environmental conditions. Feasible field microbial remediation technologies for oil spill pollution in the shorelines mainly include the addition of high-efficiency oil degrading bacteria (immobilized bacteria), nutrients, biosurfactants, and enzymes. Limitations to the field application of microbial remediation technology mainly include slow start-up, rapid failure, long remediation time, and uncontrolled environmental impact. Improving the environmental adaptability of microbial remediation technology and developing sustainable microbial remediation technology will be the focus of future research. The feasibility of microbial remediation techniques should also be evaluated comprehensively.

Oil-Contaminated Soil Remediation with Biodegradation by Autochthonous Microorganisms and Phytoremediation by Maize (Zea mays)

Biological methods are currently the most commonly used methods for removing hazardous substances from land. This research work focuses on the remediation of oil-contaminated land. The biodegradation of aliphatic hydrocarbons and PAHs as a result of inoculation with biopreparations B1 and B2 was investigated. Biopreparation B1 was developed on the basis of autochthonous bacteria, consisting of strains Dietzia sp. IN118, Gordonia sp. IN101, Mycolicibacterium frederiksbergense IN53, Rhodococcus erythropolis IN119, Rhodococcus globerulus IN113 and Raoultella sp. IN109, whereas biopreparation B2 was enriched with fungi, such as Aspergillus sydowii, Aspergillus versicolor, Candida sp., Cladosporium halotolerans, Penicillium chrysogenum. As a result of biodegradation tests conducted under ex situ conditions for soil inoculated with biopreparation B1, the concentrations of TPH and PAH were reduced by 31.85% and 27.41%, respectively. Soil inoculation with biopreparation B2 turned out to be more effective, as a result of which the concentration of TPH was reduced by 41.67% and PAH by 34.73%. Another issue was the phytoremediation of the pre-treated G6-3B2 soil with the use of Zea mays. The tests were carried out in three systems (system 1-soil G6-3B2 + Zea mays; system 2-soil G6-3B2 + biopreparation B2 + Zea mays; system 3-soil G6-3B2 + biopreparation B2 with γ-PGA + Zea mays) for 6 months. The highest degree of TPH and PAH reduction was obtained in system 3, amounting to 65.35% and 60.80%, respectively. The lowest phytoremediation efficiency was recorded in the non-inoculated system 1, where the concentration of TPH was reduced by 22.80% and PAH by 18.48%. Toxicological tests carried out using PhytotoxkitTM, OstracodtoxkitTM and Microtox® Solid Phase tests confirmed the effectiveness of remediation procedures and showed a correlation between the concentration of petroleum hydrocarbons in the soil and its toxicity. The results obtained during the research indicate the great potential of bioremediation practices with the use of microbial biopreparations and Zea mays in the treatment of soils contaminated with petroleum hydrocarbons.

Response of the soil microbial community to petroleum hydrocarbon stress shows a threshold effect: research on aged realistic contaminated fields

Introduction

Microbes play key roles in maintaining soil ecological functions. Petroleum hydrocarbon contamination is expected to affect microbial ecological characteristics and the ecological services they provide. In this study, the multifunctionalities of contaminated and uncontaminated soils in an aged petroleum hydrocarbon-contaminated field and their correlation with soil microbial characteristics were analyzed to explore the effect of petroleum hydrocarbons on soil microbes.

Methods

Soil physicochemical parameters were determined to calculate soil multifunctionalities. In addition, 16S high-throughput sequencing technology and bioinformation analysis were used to explore microbial characteristics.

Results

The results indicated that high concentrations of petroleum hydrocarbons (565-3,613 mg•kg^-1, high contamination) reduced soil multifunctionality, while low concentrations of petroleum hydrocarbons (13-408 mg•kg^-1, light contamination) might increase soil multifunctionality. In addition, light petroleum hydrocarbon contamination increased the richness and evenness of microbial community (p < 0.01), enhanced the microbial interactions and widened the niche breadth of keystone genus, while high petroleum hydrocarbon contamination reduced the richness of the microbial community (p < 0.05), simplified the microbial co-occurrence network, and increased the niche overlap of keystone genus.

Conclusion

Our study demonstrates that light petroleum hydrocarbon contamination has a certain improvement effect on soil multifunctionalities and microbial characteristics. While high contamination shows an inhibitory effect on soil multifunctionalities and microbial characteristics, which has significance for the protection and management of petroleum hydrocarbon-contaminated soil.

Nutritional additives dominance in driving the bacterial communities succession and bioremediation of hydrocarbon and heavy metal contaminated soil microcosms

Soil quality and microbial diversity are essential to the health of ecosystems. However, it is unclear how the use of eco-friendly natural additives can improve the quality and microbial diversity of contaminated soils. Herein, we used high-throughput 16 S rDNA amplicon Illumina sequencing to evaluate the stimulation and development of microbial diversity and concomitant bioremediation in hydrocarbon (HC) and heavy metal (HM)-rich waste disposal site soil when treated with meat and bone meal (MBM), cyclodextrin (Cdx), and MBM and cyclodextrin mixture (Cdx MBM) over a period of 3 months. Results showed that natural additive treatments significantly increased the soil bacterial diversity (higher Shannon index, Simpson index and evenness) in a time-dependent manner, with Cdx eliciting the greatest enhancement. The two additives influenced the bacterial community succession patterns differently. MBM, while it enhanced the enrichment of specific genera Chitinophaga and Terrimonas, did not significantly alter the total bacterial community. In contrast, Cdx or Cdx MBM promoted a profound change of the bacteria community over time, with the enrichment of the genera Parvibaculum, Arenimonas and unclassified Actinobacteria. These results provide evidence on the involvement of the two natural additives in coupling HC and HM bioremediation and bacterial community perturbations, and thus illustrates their potential application in ecologically sound bioremediation technologies for contaminated soils.

Development of a duplex q-PCR for the simultaneous detection of Parachlamydia acanthamoebae and Simkania negevensis in environmental and clinical samples

Parachlamydia acanthamoebae and Simkania negevensis, two Chlamydia-like bacteria, have been recently recognized as emerging human respiratory pathogens. The prevalence and frequency of these bacteria in the environment and among atypical pneumonia patients are still underestimated by classical cultures, immunohistochemistry and serology which are non-specific, long and tedious methods. This study aims to develop a new duplex probe-based q-PCR assay for the simultaneous detection and quantification of P. acanthamoebae and S. negevensis. The selected hydrolysis probes displayed no cross-reaction with the closely related Chlamydia or the other tested waterborne pathogens. The assay achieved a large dynamic range for quantification (from 5 × 10⁶ to 5 DNA copies/reaction). Efficiencies of FAM and JOE label probes weren't affected when they were combined. They were close to 100%, indicating the linear amplification. The application of this diagnostic tool resulted in 9/47 (19%) and 4/47 (8.5%) positive water samples for P. acanthamoebae and S. negevensis, respectively. P. acanthamoebae was also covered from 2/78 (2.5%) respiratory specimens and only one case (1/200 = 0.5%) of P. acanthamoebae and SARS-CoV-2 co-infection was noticed. While S. negevensis wasn't detected in clinical samples, the developed duplex q-PCR was shown to be an accurate, highly sensitive, and robust diagnostic tool for the detection and quantification of P. acanthamoebae and S. negevensis.

A new TaqMan real-time PCR assay to detect Parachlamydia acanthamoebae and to monitor its co-existence with SARS-COV-2 among COVID-19 patients

Human respiratory infections caused by a large variety of microbial pathogens are the most common diseases responsible for hospitalization, morbidity and mortality. Parachlamydia acanthamoebae, a Chlamydia-related bacterium, has been found to be potentially associated with these diseases. An early and accurate diagnosis of this pathogen could be useful to avoid the potential respiratory complications linked especially to COVID-19 patients and to set suitable outbreak control measures. A TaqMan-PCR assay was developed to detect and quantify Parachlamydia acanthamoebae in environmental and clinical samples from patients of all ages with COVID-19. The selected hydrolysis probe displayed no cross-reaction with the closely related Chlamydia or the other tested pathogens. This q-PCR achieved good reproducibility and repeatability with a detection limit of about 5 DNA copies per reaction. Using this q-PCR assay, Parachlamydia acanthamoebae was detected in 2/78 respiratory specimens and 9/47 water samples. Only one case (1.3%) of Parachlamydia acanthamoebae and SARS-COV-2 co-infection was noticed. To our knowledge, the combination of these two respiratory pathogens has not been described yet. This new TaqMan-PCR assay represents an efficient diagnostic tool to survey Parachlamydia acanthamoebae on a large-scale screening programs and also during outbreaks.

Rapid method for detection, quantification and measuring microbial degradation of pesticide-thiram using high performance thin layer chromatography (HPTLC)

Thiram (tetramethylthiuramdisulfide) or thiram sulphide is a dithiocarbamate group of non-systemic group of fungicide which are applied for seed treatment, control of the crop pests, to repel animals, etc. Moreover, thiram has also been responsible to cause moderate skin sensitivity and eye irritation. Higher exposure to thiram might also lead to developmental damages to newborn and neurotoxic effects to non-target organisms. Advancing to prevent such toxic effects and prevention of soil fertility from thiram and thiram-like chemicals is indispensable. The analytical High-Performance Thin-Layer Chromatography (HPTLC) is a simple, quick and a reliable method was proposed and validated for the detection and quantification of various small molecules for many years. This manuscript represents the solution to use microbes to degrade the thiram present in the soil and for that, HPTLC based method to study thiram degradation by Pseudomonas has been designed. Herein, a HPTLC protocol formalised to reveal the detection and quantification of thiram within the range of 100 to 700 ng/spot on TLC plate. The same concentration was then used for calculating percent microbial degradation of thiram from the culture broth. To perform the microbial degradation of thiram, Pseudomonas otitidis strain TD-8 and Pseudomonas stutzeri strain TD-18 were taken as thiram degrader microbial strain. The efficacy of TD-8 to degrade thiram was identified to be 81 and 99% when grown in presence of thiram for 4 days and 8 days, respectively, while TD-18 strain's efficacy to degrade thiram was found to be 57% and 99% when grown in presence of thiram for 4 days and 8 days, respectively.

Hydrocarbons removal from real marine sediments: Analysis of degradation pathways and microbial community development during bioslurry treatment

In this study, real marine sediments polluted by petroleum compounds were treated by means of a bioslurry pilot scale reactor. The treatment performance was evaluated by measuring the removal of total petroleum hydrocarbon (TPH), coupled to further analyses required to understand the mechanisms involved in the biodegradation process. The maximum TPH-removal efficiency reached 86 % at the end of experiments. Moreover, high throughput 16S RNA gene sequencing was used to describe the microbiome composition in sediment prior to, and after, bioslurry treatment, in order to identify the taxa mostly entailed in the TPH removal process. The raw sediment was mostly colonized by members of Sulfurimonas genus; after bioslurry treatment, it was noticed a shift in the microbial community composition, with Proteobacteria phylum dominating the remediation environment (high increase in terms of growth for Hydrogenophaga and Sphingorhabdus genera) along with the Phaeodactylibacter genus (Bacteroidetes). Furthermore, the assessment of gaseous emissions from the system allowed to quantify the volatile hydrocarbon component and, consequently, to obtain a more accurate evaluation of TPH-removal pathway by the bioslurry system. Finally, phytotoxicity tests on sediment samples highlighted an increase of the treated sample quality status compared to the untreated one.

Indigenous oil-degrading bacteria more efficient in soil bioremediation than microbial consortium and active even in super oil-saturated soils

A microbial consortium of the hydrocarbonoclastic bacterial species, comprising Actinotalea ferrariae, Arthrobacter ginsengisoli, Dietzia cinnamea, Dietzia papillomatosis, and Pseudomonas songnenensis, isolated from oil-saturated desert soil did not consume more oil in batch cultures than the individual species with the maximum oil consumption. In oil-polluted desert soil microcosms, the rate of oil removal in the soil samples bioaugmented with the microbial consortium was similar to the rate of oil removal in the unbioaugmented ones through a 6-month bioremediation experiment. Although the composition of hydrocarbonoclastic bacterial communities in the unbioaugmented and bioaugmented soil samples was different, the predominant bacterial species during most of the months were the same. Toward the end of the bioremediation experiment, Ar. ginsengisoli prevailed in both soil samples, suggesting its important role in oil removal. Self-cleaning proceeded in desert soil samples artificially polluted with 1, 10, 20, and 30% of crude oil and incubated at 30 °C for 6 months. Oil was removed effectively at rates reaching 73.6 and 69.3% in the soils polluted with 1 and 10% oil concentrations, respectively, and reached 50% in desert soils polluted with 20 and 30% oil concentrations. The bacterial numbers increased in all soil samples from hundreds of thousands per gram of soil samples at time zero to millions and tens of millions per gram of soil samples after 6 months. It was concluded that bioaugmenting oil-polluted soil samples with microbial consortium of hydrocarbonoclastic bacterial species with high oil removal potential did not drastically enhance oil bioremediation and that even in super oil-saturated soils, indigenous oil-degrading bacteria will prevail and effectively contribute to oil removal from the surrounding environment.

Primary microbial succession in the anchialine ecosystem

When new land is created, initial microbial colonization lays the foundation for further ecological succession of plant and animal communities. Primary microbial succession of new aquatic habitats formed during volcanic activity has received little attention. The anchialine ecosystem, which includes coastal ponds in young lava flows, offers an opportunity to examine this process. Here, we characterized microbial communities of anchialine habitats in Hawaii that were created during volcanic eruptions in 2018. Benthic samples from three habitats were collected ∼2 years after their formation and at later time points spanning ∼1 year. Sequence profiling (16S and 18S) of prokaryotic and eukaryotic communities was used to test whether communities were similar to those from older, established anchialine habitats, and if community structure changed over time. Results show that microbial communities from the new habitats were unlike any from established anchialine microbial communities, having higher proportions of Planctomycetota and Chloroflexi but lower proportions of green algae. Each new habitat also harbored its own unique community relative to other habitats. While community composition in each habitat underwent statistically significant changes over time, they remained distinctive from established anchialine habitats. New habitats also had highly elevated temperatures compared to other habitats. These results suggest idiosyncratic microbial consortia form during early succession of Hawaiian anchialine habitats. Future monitoring will reveal whether the early communities described here remain stable after temperatures decline and macro-organisms become more abundant, or if microbial communities will continue to change and eventually resemble those of established habitats. This work is a key first step in examining primary volcanic succession in aquatic habitats and suggests young anchialine habitats may warrant special conservation status.

Optimization of biomass production by autochthonous Pseudomonas sp. MT1A3 as strategy to apply bioremediation in situ in a chronically hydrocarbon-contaminated soil

These days, petroleum hydrocarbon pollution has become a global problem, because of this, bioremediation is presented as a strategy for cleaning up sites contaminated with organic pollutants, and it has an increasing role in relation to the potential it presents as a non-invasive and cost-effective technology. The aim of this study is to optimize the biomass production of Pseudomonas sp. MT1A3 strain as a soil bioremediation approach for petroleum hydrocarbon polluted environments. Factorial experimental designs were employed to study the effect of several factors of composition medium and incubation conditions on biomass production. Agro-industrial wastes such as peanut oil as carbon source, NaNO₃ as nitrogen source and incubation temperature were found to be significant independent variables. These factors were further optimized using Box-Behnken design. Combination of peanut oil 18.69 g/L, NaNO₃ 2.39 g/L and 26.06 °C incubation temperature was optimum for maximum biomass production of MT1A3 and the model validated in a bioreactor allowed to obtain 9.67 g/L. Based on these results, this autochthonous strain was applied in bioaugmentation as a bioremediation strategy through microcosm designs, reaching 93.52% of total hydrocarbon removal at 60 days. This constitutes a promising alternative for hydrocarbon-contaminated soil.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-022-03183-6.

Evaluating the aerobic xylene-degrading potential of the intrinsic microbial community of a legacy BTEX-contaminated aquifer by enrichment culturing coupled with multi-omics analysis: uncovering the role of Hydrogenophaga strains in xylene degradation

To develop effective bioremediation strategies, it is always important to explore autochthonous microbial community diversity using substrate-specific enrichment. The primary objective of this present study was to reveal the diversity of aerobic xylene-degrading bacteria at a legacy BTEX-contaminated site where xylene is the predominant contaminant, as well as to identify potential indigenous strains that could effectively degrade xylenes, in order to better understand the underlying facts about xylene degradation using a multi-omics approach. Henceforward, parallel aerobic microcosms were set up using different xylene isomers as the sole carbon source to investigate evolved bacterial communities using both culture-dependent and independent methods. Research outcome showed that the autochthonous community of this legacy BTEX-contaminated site has the capability to remove all of the xylene isomers from the environment aerobically employing different bacterial groups for different xylene isomers. Interestingly, polyphasic analysis of the enrichments disclose that the community composition of the o-xylene-degrading enrichment community was utterly distinct from that of the m- and p-xylene-degrading enrichments. Although in each of the enrichments Pseudomonas and Acidovorax were the dominant genera, in the case of o-xylene-degrading enrichment Rhodococcus was the main player. Among the isolates, two Hydogenophaga strains, belonging to the same genomic species, were obtained from p-xylene-degrading enrichment, substantially able to degrade aromatic hydrocarbons including xylene isomers aerobically. Comparative whole-genome analysis of the strains revealed different genomic adaptations to aromatic hydrocarbon degradation, providing an explanation on their different xylene isomer-degrading abilities.

Preliminary insights about the treatment of contaminated marine sediments by means of bioslurry reactor: Process evaluation and microbiological characterization

Contaminated marine sediments represent a critical threat towards human health and ecosystems, since they constitute a potential reservoir of toxic compounds release. In the present study, a bioslurry reactor was studied for the treatment of real marine sediments contaminated by petroleum hydrocarbons. The experimental campaign was divided in two periods: in the first period, microcosm trials were carried out to achieve useful indicators for biological hydrocarbon removal from sediments. The microcosm trials highlighted that the inoculum of halotolerant allochthonous bacteria provided the highest performance followed by autochthonous biomass. Based on the achieved results, in the second experimental period a bioslurry reactor was started up, based on a semisolid stirred tank reactor (STR) operated in batch mode. The process performances have been evaluated in terms of total petroleum hydrocarbon (TPH) removal, coupled with the characterization of microbial community through a Next Generation Sequencing (NGS) and phytotoxicity tests through the Germination Index (GI) with Lepidium Sativum seeds. The achieved results showed good hydrocarbons removal, equal to 40%, with a maximum removal rate of 220 mg_TPH kg^-1 d^-1, but highlighting that high contaminant concentrations might affect negatively the overall removal performance. In general, the observed results were encouraging towards the feasibility of biological treatment of marine sediments contaminated by hydrocarbons. The microbiological analysis allowed the identification of taxa most involved in the degradation of TPH, highlighting after the treatment a shift in the microbial community from that of the raw sediment.

Metagenomic Analysis for Evaluating Change in Bacterial Diversity in TPH-Contaminated Soil after Soil Remediation

Soil washing and landfarming processes are widely used to remediate total petroleum hydrocarbon (TPH)-contaminated soil, but the impact of these processes on soil bacteria is not well understood. Four different states of soil (uncontaminated soil (control), TPH-contaminated soil (CS), after soil washing (SW), and landfarming (LF)) were collected from a soil remediation facility to investigate the impact of TPH and soil remediation processes on soil bacterial populations by metagenomic analysis. Results showed that TPH contamination reduced the operational taxonomic unit (OTU) number and alpha diversity of soil bacteria. Compared to SW and LF remediation techniques, LF increased more bacterial richness and diversity than SW, indicating that LF is a more effective technique for TPH remediation in terms of microbial recovery. Among different bacterial species, Proteobacteria were the most abundant in all soil groups followed by Actinobacteria, Acidobacteria, and Firmicutes. For each soil group, the distribution pattern of the Proteobacteria class was different. The most abundant classed were Alphaproteobacteria (16.56%) in uncontaminated soils, Deltaproteobacteria (34%) in TPH-contaminated soils, Betaproteobacteria (24%) in soil washing, and Gammaproteobacteria (24%) in landfarming, respectively. TPH-degrading bacteria were detected from soil washing (23%) and TPH-contaminated soils (21%) and decreased to 12% in landfarming soil. These results suggest that soil pollution can change the diversity of microbial groups and different remediation techniques have varied effective ranges for recovering bacterial communities and diversity. In conclusion, the landfarming process of TPH remediation is more advantageous than soil washing from the perspective of bacterial ecology.

Ascomycetes versus Spent Mushroom Substrate in Mycoremediation of Dredged Sediments Contaminated by Total Petroleum Hydrocarbons: The Involvement of the Bacterial Metabolism

Two mycoremediation approaches for the depletion of the total petroleum hydrocarbons in dredged sediments were compared: co-composting with spent mushroom substrate (SMS) from Pleurotus ostreatus and bioaugmentation with Lambertella sp. MUT 5852, an ascomycetes autochthonous to the sediment, capable of utilizing diesel oil its sole carbon source. After 28 days of incubation, 99% depletion was observed in presence of Lambertella sp. MUT 5852. No total petroleum hydrocarbon depletion was observed in sediment co-composting with the SMS after 60 days of incubation. 16S rDNA metabarcoding of the bacterial community was performed to evaluate the potential synergism between fungi and bacteria in the bioremediation process. The functional metagenomic prediction approach indicated that the biodiversity of the bacterial genera potentially involved in the degradation of TPH was higher in sediment bioaugmented with Lambertella sp. MUT 5852, which resulted in being mandatory for TPH depletion. Mechanisms of co-substrate inhibition of the hydrocarburoclastic bacterial species, due to the bioavailable organic matter of the SMS, are suggested to be involved in the observed kinetics of TPH depletion, failing in the case of SMS and successful in the case of Lambertella sp. MUT 5852.

Harnessing the Potential of Native Microbial Communities for Bioremediation of Oil Spills in the Iberian Peninsula NW Coast

Oil spills are among the most catastrophic events to marine ecosystems and current remediation techniques are not suitable for ecological restoration. Bioremediation approaches can take advantage of the activity of microorganisms with biodegradation capacity thus helping to accelerate the recovery of contaminated environments. The use of native microorganisms can increase the bioremediation efficiency since they have higher potential to survive in the natural environment while preventing unpredictable ecological impacts associated with the introduction of non-native organisms. In order to know the geographical scale to which a native bioremediation consortium can be applied, we need to understand the spatial heterogeneity of the natural microbial communities with potential for hydrocarbon degradation. In the present study, we aim to describe the genetic diversity and the potential of native microbial communities to degrade petroleum hydrocarbons, at an early stage of bioremediation, along the NW Iberian Peninsula coast, an area particularly susceptible to oil spills. Seawater samples collected in 47 sites were exposed to crude oil for 2 weeks, in enrichment experiments. Seawater samples collected in situ, and samples collected after the enrichment with crude oil, were characterized for prokaryotic communities by using 16S rRNA gene amplicon sequencing and predictive functional profiling. Results showed a drastic decrease in richness and diversity of microbial communities after the enrichment with crude oil. Enriched microbial communities were mainly dominated by genera known to degrade hydrocarbons, namely Alcanivorax, Pseudomonas, Acinetobacter, Rhodococcus, Flavobacterium, Oleibacter, Marinobacter, and Thalassospira, without significant differences between geographic areas and locations. Predictive functional profiling of the enriched microbial consortia showed a high potential to degrade the aromatic compounds aminobenzoate, benzoate, chlorocyclohexane, chlorobenzene, ethylbenzene, naphthalene, polycyclic aromatic compounds, styrene, toluene, and xylene. Only a few genera contributed for more than 50% of this genetic potential for aromatic compounds degradation in the enriched communities, namely Alcanivorax, Thalassospira, and Pseudomonas spp. This work is a starting point for the future development of prototype consortia of hydrocarbon-degrading bacteria to mitigate oil spills in the Iberian NW coast.

Combined Microbial Consortium Inoculation and Black Locust Planting Is Effective in the Bioremediation of Waste Drill Cuttings

Waste drill cuttings (WDCs), produced during gas and oil drilling consisting of 80% rock cuttings and 20% drilling muds, are an increasingly potent source of environmental pollution. We studied the efficiency of bioaugmentation and phytoremediation to remediate WDCs in an experiment where WDCs were incubated in a greenhouse for 120 days with and without black locust (Robinia pseudoacacia) plant and with or without bacterial and fungal consortium inoculant. The pollutant removal rates were highest in inoculated and planted treatment, followed by inoculated treatment and planted treatment. The small decrease in contaminant level in the control treatment suggested that indigenous microorganisms in WDCs had little pollutant degradation capability. In the inoculated and planted treatments, after 120 days, the germination rate of red clover seeds was on the same level as in the natural soil, showing a marked decrease in the ecotoxicity of WDC. Both the bacterial and fungal richness and bacterial diversity increased in all the treatments over time, whereas fungal diversity increased only in the not-inoculated treatments. The activity of laccase enzyme played a key role in the bioremediation process. The enzyme activities were mostly governed by inoculated consortium and soil bacterial community, and black locust affected the bioremediation mainly through its effect on N content that further affected bacterial and fungal communities.

Effect of oxygen limitation on the enrichment of bacteria degrading either benzene or toluene and the identification of Malikia spinosa (Comamonadaceae) as prominent aerobic benzene-, toluene-, and ethylbenzene-degrading bacterium: enrichment, isolation and whole-genome analysis

The primary aims of this present study were to evaluate the effect of oxygen limitation on the bacterial community structure of enrichment cultures degrading either benzene or toluene and to clarify the role of Malikia-related bacteria in the aerobic degradation of BTEX compounds. Accordingly, parallel aerobic and microaerobic enrichment cultures were set up and the bacterial communities were investigated through cultivation and 16S rDNA Illumina amplicon sequencing. In the aerobic benzene-degrading enrichment cultures, the overwhelming dominance of Malikia spinosa was observed and it was abundant in the aerobic toluene-degrading enrichment cultures as well. Successful isolation of a Malikia spinosa strain shed light on the fact that this bacterium harbours a catechol 2,3-dioxygenase (C23O) gene encoding a subfamily I.2.C-type extradiol dioxygenase and it is able to degrade benzene, toluene and ethylbenzene under clear aerobic conditions. While quick degradation of the aromatic substrates was observable in the case of the aerobic enrichments, no significant benzene degradation, and the slow degradation of toluene was observed in the microaerobic enrichments. Despite harbouring a subfamily I.2.C-type C23O gene, Malikia spinosa was not found in the microaerobic enrichments; instead, members of the Pseudomonas veronii/extremaustralis lineage dominated these communities. Whole-genome analysis of M. spinosa strain AB6 revealed that the C23O gene was part of a phenol-degrading gene cluster, which was acquired by the strain through a horizontal gene transfer event. Results of the present study revealed that bacteria, which encode subfamily I.2.C-type extradiol dioxygenase enzyme, will not be automatically able to degrade monoaromatic hydrocarbons under microaerobic conditions.

Potential use of biochar and rhamnolipid biosurfactant for remediation of crude oil-contaminated coastal wetland soil: Ecotoxicity assessment

Remediation of wetland soils contaminated with petroleum hydrocarbons is a challenging task. Biosurfactant and biochar have been used in oil remediation. However, little is known about the ecotoxicity of these materials when applied in wetland ecosystems. In this study, the ecotoxicity of biochar and rhamnolipid (RL) biosurfactant as crude oil remediation strategies in a Louisiana wetland soil was investigated. A pot experiment was set up with wetland soil treated with/without crude oil followed by subjecting to application of 1% biochar and various levels of RL ranging from 0.1% to 1.4%. The ecotoxicity was evaluated regarding to high plant (S. Alterniflora), algae, and soil microbes. Specifically, after a 30-day growth in a controlled chamber, plant biomass change as well as shoot/root ratio was measured. Algae growth was estimated by quantifying chlorophyll by spectrometry following separation, and soil microbial community was characterized by phospholipid fatty acids analysis. Results showed that plant can tolerate RL level up to 0.8%, while algae growth was strongly inhibited at RL > 0.1%. Algal biomass was significantly increased by biochar, which offset the negative impact of oil and RL. Additionally, soil microbial community shift caused by crude oil and RL was alleviated by biochar with promoting Gram-positive bacteria, actinomycetes, and arbuscular mycorrhizal fungi. Overall, this study shows that integrated treatment of biochar and RL has the lowest ecotoxicity to plant and algae when used in oil remediation of contaminated wetland soils.

Aerobic and oxygen-limited naphthalene-amended enrichments induced the dominance of Pseudomonas spp. from a groundwater bacterial biofilm

In this study, we aimed at determining the impact of naphthalene and different oxygen levels on a biofilm bacterial community originated from a petroleum hydrocarbon-contaminated groundwater. By using cultivation-dependent and cultivation-independent approaches, the enrichment, identification, and isolation of aerobic and oxygen-limited naphthalene degraders was possible. Results indicated that, regardless of the oxygenation conditions, Pseudomonas spp. became the most dominant in the naphthalene-amended selective enrichment cultures. Under low-oxygen conditions, P. veronii/P. extremaustralis lineage affiliating bacteria, and under full aerobic conditions P. laurentiana-related isolates were most probably capable of naphthalene biodegradation. A molecular biological tool has been developed for the detection of naphthalene 1,2-dioxygenase-related 2Fe-2S reductase genes of Gram-negative bacteria. The newly developed COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOP-PCR) technique may be used in the monitoring of the natural attenuation capacity of PAH-contaminated sites. A bacterial strain collection with prolific biofilm-producing and effective naphthalene-degrading organisms was established. The obtained strain collection may be applicable in the future for the development of biofilm-based bioremediation systems for the elimination of PAHs from groundwater (e.g., biofilm-based biobarriers).

Biodegradation of methyl and butylparaben by bacterial strains isolated from amended and non-amended agricultural soil. Identification, behavior and enzyme activities of microorganisms

The aim of the present study was to investigate the kinetics of methylparaben (MPB) and butylparaben (BPB) removal, two emerging pollutants with possible endocrine disrupting effects, from agricultural soil with and without amendment with compost from sewage sludge used as biostimulant. Compound removal is explained by a first-order kinetic model with half-life times of 6.5/6.7 days and 11.4/8.2 days, in presence/absence of compost, for MPB and BPB respectively. % R² for the fitted model were higher than 96% in all cases. Additionally, isolation of bacteria capable to grow using MPB or BPB as carbon source was also carry out. Laboratory tests demonstrated the ability of these bacteria to biodegrade MPB and BPB from culture media in more than 95% in some cases. These strains showed high ability to biodegrade the compounds. Ten isolates, most of them related to Gram positive bacteria of the genus Bacillus, were identified by 16S rRNA gene sequencing. The study of the enzymatic activities of the isolates revealed both esterase (C4) and esterase-lipase activities.

Impact of Crude Oil on Functional Groups of Culturable Bacteria and Colonization of Symbiotic Microorganisms in the <i>Clitoria-Brachiaria</i> Rhizosphere Grown in Mesocosms

This research evaluated the changes on populations of culturable N-fixing free bacteria (NFFB) and P-solubilizing bacteria (PSB), as well as on the root nodulation by native rhizobia, the root colonization and spore number of arbuscular mycorrhizal fungi (AMF), in the rhizosphere of Clitoria ternatea and Brachiaria brizantha grown in mesocosms contaminated with crude oil (0, 3000, 6000, 9000, and 12000 mg kg-1), for 240 days. After 24 h of soil contamination, the highest populations of NFFB and PSB (5.5 and 4.9 LogUFC, respectively) were found in control, and the lowest populations were obtained at 12000 mg kg-1 (5.1 and 4.2 LogUFC, respectively). In contrast, at 60 and 240 days, the control showed lower populations of NFFB and PSB (5.4 and 4.8 LogUFC, respectively) than contaminated treatments. The highest number or root nodules in C. ternatea was quantified in control at 60 and 240 days (25 and 27 nodules, respectively) in comparison to those observed at the treatment with 12000 mg kg-1 (7 and 1 nodule, respectively). At 60 days, AMF colonization in both plant species, and the number of spores significantly decreased as the crude oil concentration increased; however, at 240 days, the highest number of AMF spores was recorded at treatments with 6000 and 12000 mg kg-1. The dry weight of both plant species significantly decreased as crude oil concentrations increased. Although C. ternatea was more susceptible to the toxic effects of crude oil, this plant species showed greater content of total chlorophyll than B. brizantha.

Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities

Disturbance is known to affect the ecosystem structure, but predicting its outcomes remains elusive. Similarly, community diversity is believed to relate to ecosystem functions, yet the underlying mechanisms are poorly understood. Here, we tested the effect of disturbance on the structure, assembly, and ecosystem function of complex microbial communities within an engineered system. We carried out a microcosm experiment where activated sludge bioreactors operated in daily cycles were subjected to eight different frequency levels of augmentation with a toxic pollutant, from never (undisturbed) to every day (press-disturbed), for 35 days. Microbial communities were assessed by combining distance-based methods, general linear multivariate models, α-diversity indices, and null model analyses on metagenomics and 16S rRNA gene amplicon data. A stronger temporal decrease in α-diversity at the extreme, undisturbed and press-disturbed, ends of the disturbance range led to a hump-backed pattern, with the highest diversity found at intermediate levels of disturbance. Undisturbed and press-disturbed levels displayed the highest community and functional similarity across replicates, suggesting deterministic processes were dominating. The opposite was observed amongst intermediately disturbed levels, indicating stronger stochastic assembly mechanisms. Trade-offs were observed in the ecosystem function between organic carbon removal and both nitrification and biomass productivity, as well as between diversity and these functions. Hence, not every ecosystem function was favoured by higher community diversity. Our results show that the assessment of changes in diversity, along with the underlying stochastic–deterministic assembly processes, is essential to understanding the impact of disturbance in complex microbial communities.

Complex microbial communities and ecosystems are highly sensitive to disturbance, which can affect community diversity and structure, but to date the impact of disturbance remains difficult to predict. Here, Stefan Wuertz and colleagues from the Nanyang Technological University in Singapore show how different disturbance frequencies affect microbial population dynamics. Analyses of microbial communities in sludge bioreactors exposed to a toxic pollutant at different rates revealed that populations at the extremes (not exposed and most exposed) showed the lowest α-diversity, whereas populations exposed at intermediate levels were most diverse. Notably, ecosystem function trade-offs were observed between organic carbon removal and nitrification and biomass productivity, with diversity also affecting these functions. These observations highlight the importance of evaluating diversity when determining the effects of disturbance on microbial communities.

Tolerance and phytoremediation potential of four tropical grass species to land-applied drill cuttings

This work evaluated the tolerance and phytoremediation potential of four tropical grasses over a 12-week period, with a view to assessing their suitability for land farming of oil-based drill cuttings. It considered four grass species, namely, guinea grass (Megathyrsus maximus), spear grass (Imperata cylindrica), gamba grass (Andropogon gayanus), and elephant grass (Pennisetum purpureum). The treatments involved growing each of the four grasses on a mixture of 3:1 soil/drill-cuttings ratio, after failed trials with mix ratios ranging from 1:3 to 2:1 soil/drill-cuttings ratio, and on uncontaminated soil. The TPH concentration dropped by 27-81% from 4805 mg kg^-1 in the 3:1 soil/drill-cuttings mixtures in the different treatments after 12 weeks. Better growth performance in the contaminated treatments, compared to uncontaminated controls, correlated with higher reduction in TPH and metals concentrations. The contaminated elephant grass treatment showed better plant height and leaf sizes than the uncontaminated control. The growth parameters of contaminated treatments with the other three grasses ranged from 29 to 75% of the corresponding uncontaminated controls. The results demonstrate that the relative suitability of the grasses for land farming of oil-based drill cuttings is in the order, elephant grass > guinea grass > gamba grass > spear grass.

Responses and roles of roots, microbes, and degrading genes in rhizosphere during phytoremediation of petroleum hydrocarbons contaminated soil

Rhizodegradation performed by plant roots and the associated bacteria is one of the major mechanisms that contribute to removal of petroleum hydrocarbons (PHCs) during phytoremediation. In this study, the pot-culture experiment using wild ornamental Hylotelephium spectabile (Boreau) H. Ohba was designed to explore responses and roles of roots, microbes, and degrading genes in the rhizodegradation process. Results showed that PHCs degradation rate by phytoremediation was up to 37.6-53.3% while phytoaccumulation accounted for a low proportion, just at 0.3-13.3%. A total of 37 phyla were classified through the high throughput sequencing, among which Proteobacteria, Actinobacteria, and Acidobacteria were the three most dominant phyla, accounting for >60% of the phylum frequency. The selective enrichment of PHC degraders with high salt-tolerance, including Alcanivorax and Bacteroidetes, was induced. Generally, relative abundance of the PHC degrading genes increased significantly with an increase in PHCs concentrations, and the gene copy number in the phytoremediation group was 1.46-14.44 times as much as that in the unplanted controls. Overall, the presence of PHCs and plant roots showed a stimulating effect on the development of specific degraders containing PHC degrading genes, and correspondingly, a biodegradation-beneficial community structure had been constructed to contribute to PHCs degradation in the rhizosphere.

Aerobic and oxygen-limited enrichment of BTEX-degrading biofilm bacteria: dominance of Malikia versus Acidovorax species

Due to their high resistance against environmental challenges, bacterial biofilms are ubiquitous and are frequently associated with undesired phenomena in environmental industry (e. g. biofouling). However, because of the high phylogenetic and functional diversity, bacterial biofilms are important sources of biotechnologically relevant microorganisms, e.g. those showing bioremediation potential. In our previous work, the high phylogenetic and metabolic diversity of a clogging biofilm, developed in a simple aromatic hydrocarbon (BTEX)-contaminated groundwater well was uncovered. The determination of relationships between different groups of biofilm bacteria and certain metabolic traits has been omitted so far. Therefore, by setting up new biofilm-based enrichment microcosms, the research goal of the present study was to identify the aerobic/hypoxic BTEX-degrading and/or prolific biofilm-forming bacteria. The initial bacterial community composition as well as temporal dynamics due to the selective enrichment has been determined. The obtained results indicated that the concentration of dissolved oxygen may be a strong selective force on the evolution and final structure of microbial communities, developed in hydrocarbon-contaminated environments. Accordingly, members of the genus Malikia proved to be the most dominant community members of the aerobic BTEX-degrading enrichments. Acidovorax spp. dominated the oxygen-limited/hypoxic setup. During the study, a strain collection of 23 different bacterial species was obtained. Non-pathogenic members of this strain collection, with outstanding biodegradation (e.g. Pseudomonas, Variovorax isolates) and biofilm-forming potential (e.g. Rhizobium), may potentially be applied in the development of biofilm-based semipermeable reactive biobarriers.

Biodegradation of Endocrine-Disrupting Chemicals and Residual Organic Pollutants of Pulp and Paper Mill Effluent by Biostimulation

Effluent discharged from the pulp and paper industry contains various refractory and androgenic compounds, even after secondary treatment by activated processes. Detailed knowledge is not yet available regarding the properties of organic pollutants and methods for their bioremediation. This study focused on detecting residual organic pollutants of pulp and paper mill effluent after biological treatment and assessing their degradability by biostimulation. The major compounds identified in the effluent were 2,3,6-trimethylphenol, 2-methoxyphenol (guaiacol), 2,6-dimethoxyphenol (syringol), methoxycinnamic acid, pentadecane, octadecanoic acid, trimethylsilyl ester, cyclotetracosane, 5,8-dimethoxy-6-methyl-2,4-bis(phenylmethyl)napthalen-1-ol, and 1,2-benzendicarboxylic acid diisononyl ester. Most of these compounds are classified as endocrine-disrupting chemicals and environmental toxicants. Some compounds are lignin monomers that are metabolic products from secondary treatment of the discharged effluent. This indicated that the existing industrial process could not further degrade the effluent. Supplementation by carbon (glucose 1.0%) and nitrogen (peptone 0.5%) bio-stimulated the degradation process. The degraded sample after biostimulation showed either disappearance or generation of metabolic products under optimized conditions, i.e., a stirring rate of 150 rpm and temperature of 37 ± 1°C after 3 and 6 days of bacterial incubation. Isolated potential autochthonous bacteria were identified as Klebsiella pneumoniae IITRCP04 (KU715839), Enterobacter cloacae strain IITRCP11 (KU715840), Enterobacter cloacae IITRCP14 (KU715841), and Acinetobacter pittii strain IITRCP19 (KU715842). Lactic acid, benzoic acid, and vanillin, resulting from residual chlorolignin compounds, were generated as potential value-added products during the detoxification of effluent in the biostimulation process, supporting the commercial importance of this process.

Characterization of bacterial community structure in a hydrocarbon-contaminated tropical African soil

The bacterial community structure in a hydrocarbon-contaminated Mechanical Engineering Workshop (MWO) soil was deciphered using 16S rRNA gene clone library analysis. Four hundred and thirty-seven clones cutting across 13 bacterial phyla were recovered from the soil. The representative bacterial phyla identified from MWO soil are Proteobacteria, Bacteroidetes, Chloroflexi, Acidobacteria, Firmicutes, Actinobacteria, Verrucomicrobia, Planctomycetes, Ignavibacteriae, Spirochaetes, Chlamydiae, Candidatus Saccharibacteria and Parcubacteria. Proteobacteria is preponderant in the contaminated soil (51.2%) with all classes except Epsilonproteobacteria duly represented. Rarefaction analysis indicates 42%, 52% and 77% of the clone library is covered at the species, genus and family/class delineations with Shannon diversity (H') and Chao1 richness indices of 5.59 and 1126, respectively. A sizeable number of bacterial phylotypes in the clone library shared high similarities with strains previously described to be involved in hydrocarbon biodegradation. Novel uncultured genera were identified that have not been previously reported from tropical African soil to be associated with natural attenuation of hydrocarbon pollutants. This study establishes the involvement of a wide array of physiologically diverse bacterial groups in natural attenuation of hydrocarbon pollutants in soil.

Advancement in LH-PCR methodology for multiple microbial species detections in fermented foods

The length-heterogeneity PCR is a low throughput molecular biology methods explored to monitor bacteria populations in different environments. It could be more used in food microbiology analysis, not only for fingerprinting analysis, but it has been hampered until now by a limiting factor which relates to the high percentage of secondary peaks. With the aim to overcome this problem, different experiments were performed focusing on changing PCR parameters in order to obtain more specific amplicon patterns and also to reduce the complexity of community patterns. With this purpose, different annealing temperatures were tested on complex fermented food matrices taken from both animal and vegetable origin and also on the bacteria isolated from the same food source. In particular, the optimal annealing temperature identified for the fermented food samples is 59 °C and the optimal for bacterial strains varied between 63 °C and 65 °C. The approach allowed the modification of the LH-PCR protocol increasing the amplification efficiency and therefore the bacteria species discrimination. These temperatures also allowed the implementation of the previous LH-PCR published database. The modification in the level of accuracy of the LH-PCR technique could also allow an improvement in the relative species quantification by the peak area evaluation.

Investigating the Microbial Degradation Potential in Oil Sands Fluid Fine Tailings Using Gamma Irradiation: A Metagenomic Perspective

Open-pit mining of the Athabasca oil sands has generated large volumes of waste termed fluid fine tailings (FFT), stored in tailings ponds. Accumulation of toxic organic substances in the tailings ponds is one of the biggest concerns. Gamma irradiation (GI) treatment could accelerate the biodegradation of toxic organic substances. Hence, this research investigates the response of the microbial consortia in GI-treated FFT materials with an emphasis on changes in diversity and organism-related stimuli. FFT materials from aged and fresh ponds were used in the study under aerobic and anaerobic conditions. Variations in the microbial diversity in GI-treated FFT materials were monitored for 52 weeks and significant stimuli (p < 0.05) were observed. Chemoorganotrophic organisms dominated in fresh and aged ponds and showed increased relative abundance resulting from GI treatment. GI-treated anaerobic FFT_aged reported stimulus of organisms with biodegradation potential (e.g., Pseudomonas, Enterobacter) and methylotrophic capabilities (e.g., Syntrophus, Smithella). In comparison, GI-treated anaerobic FFT_fresh stimulated Desulfuromonas as the principle genus at 52 weeks. Under aerobic conditions, GI-treated FFT_aged showed stimulation of organisms capable of sulfur and iron cycling (e.g., Geobacter). However, GI-treated aerobic FFT_fresh showed no stimulus at 52 weeks. This research provides an enhanced understanding of oil sands tailings biogeochemistry and the impacts of GI treatment on microorganisms as an effect for targeting toxic organics. The outcomes of this study highlight the potential for this approach to accelerate stabilization and reclamation end points. Graphical Abstract.

Bacterial interactions and implications for oil biodegradation process in mangrove sediments

Mangrove sediment harbors a unique microbiome and is a hospitable environment for a diverse group of bacteria capable of oil biodegradation. Our goal was to understand bacterial community dynamics from mangrove sediments contaminated with heavy-oil and to evaluate patterns potentially associated with oil biodegradation is such environments. We tested the previously proposed hypothesis of a two-phase pattern of petroleum biodegradation, under which key events in the degradation process take place in the first three weeks after contamination. Two sample sites with different oil pollution histories were compared through T-RFLP analyses and using a pragmatic approach based on the Microbial Resource Management Framework. Our data corroborated the already reported two-phase pattern of oil biodegradation, although the original proposed explanation related to the biophysical properties of the soil is questioned, opening the possibility to consider other plausible hypotheses of microbial interactions as the main drivers of this pattern.

Bacterial ecology of artisanal Minas cheeses assessed by culture-dependent and -independent methods

Artisanal Minas cheese is produced in Minas Gerais state, Brazil and its varieties are named according to their geographical origin (Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes). The cheese is produced with raw cow's milk and the whey from the previous cheese production ("pingo"). The high economic and cultural importance of artisanal cheese in Brazil justifies the efforts to ensure its safety, quality and provenance. This study aimed to characterize the microbial diversity composition, and geographical distribution of artisanal Minas cheese, focusing on the characterization of its autochthonous lactic acid bacteria (LAB) microbiota. Artisanal Minas cheese varieties from Serro, Canastra, Serra do Salitre, Araxá and Campo das Vertentes were analyzed by culture-dependent (culturing and LAB sequencing) and -independent (repetitive extragenic palindromic-PCR (rep-PCR) and length heterogeneity-PCR, LH-PCR) methods to characterize the microbiota. The microbial counts were variable between cheese samples, and some samples presented high number of coagulase positive bacteria and coliforms that may be associated with hygienic issues. In all samples was observed a prevalence of LAB. 16S rRNA sequencing and rep-PCR of the LAB strains identified four genus (Lactobacillus, Lactococcus, Enterococcus and Weissella), ten species and more than one strain per species. Lactobacillus was the most prevalent genera in all the cheeses. LH-PCR revealed a further six genera and ten species that were not identified by culturing, highlighting the importance of combining both culture-dependent and -independent methods to fully characterize microbiota diversity. Principal component analysis of the LH-PCR data and cluster analysis of rep-PCR data revealed that the artisanal Minas cheese microbiota was influenced not only by their geographical origin but also by the cheese farm. The lack of standardization in the milking and cheese manufacturing procedures between artisanal cheese farms could explain the microbial diversity.

Treatment of petroleum drill cuttings using bioaugmentation and biostimulation supplemented with phytoremediation

This study sought to compare the effectiveness of bioaugmentation and biostimulation, as well as the combination of both techniques, supplemented with phytoremediation, in the decontamination of petroleum drill cuttings. Drill cuttings with relatively low concentration of total petroleum hydrocarbons (TPH) and metals were mixed with soil in the ratio 5:1 and treated with three different combinations of the bioremediation options. Option A entailed bioaugmentation supplemented with phytoremediation. Option B had the combination of biostimulation and bioaugmentation supplemented with phytoremediation. While biostimulation supplemented with phytoremediation was deployed in option C. Option O containing the drill cuttings-soil mixture without treatment served as untreated control. Fertilizer application, tillage and watering were used for biostimulation treatment, while spent mushroom substrate (Pleurotus ostreatus) and elephant grass (Pennisetum purpureum) were employed for bioaugmentation and phytoremediation treatment, respectively. The drill cuttings-soil mixtures were monitored for TPH, organic carbon, total nitrogen, pH, metal concentrations, and fungal counts, over time. After 56 days of treatment, there was a decline in the initial TPH concentration of 4,114 mg kg(-1) by 5.5%, 68.3%, 75.6% and 48% in options O, A, B and C, respectively. Generally, higher TPH loss resulted from the phytoremediation treatment stage. The treated options also showed slight reductions in metal concentrations ranging from 0% to 16% of the initial low concentrations. The results highlight the effectiveness of bioaugmentation supplemented with phytoremediation. The combination of bioaugmentation and biostimulation supplemented with phytoremediation, however, may prove better in decontaminating petroleum drill cuttings to environmentally benign levels.

Microbial diversity and community structure in an antimony-rich tailings dump

To assess the impact of antimony (Sb) on microbial community structure, 12 samples were taken from an Sb tailings pile in Guizhou Province, Southwest China. All 12 samples exhibited elevated Sb concentrations, but the mobile and bioaccessible fractions were small in comparison to total Sb concentrations. Besides the geochemical analyses, microbial communities inhabiting the tailing samples were characterized to investigate the interplay between the microorganisms and environmental factors in mine tailings. In all samples, Proteobacteria and Actinobacteria were the most dominant phyla. At the genus level, Thiobacillus, Limnobacter, Nocardioides, Lysobacter, Phormidium, and Kaistobacter demonstrated relatively high abundances. The two most abundant genera, Thiobacillus and Limnobacter, are characterized as sulfur-oxidizing bacteria and thiosulfate-oxidizing bacteria, respectively, while the genus Lysobacter contains arsenic (As)-resistant bacteria. Canonical correspondence analysis (CCA) indicates that TOC and the sulfate to sulfide ratio strongly shaped the microbial communities, suggesting the influence of the environmental factors in the indigenous microbial communities.

Evaluation of microbial population and functional genes during the bioremediation of petroleum-contaminated soil as an effective monitoring approach

This study investigated the abundance and diversity of soil n-alkane and polycyclic aromatic hydrocarbon (PAH)-degrading bacterial communities. It also investigated the quantity of the functional genes, the occurrence of horizontal gene transfer (HGT) in the identified bacterial communities and the effect that such HGT can have on biostimulation process. Illumina sequencing was used to detect the microbial diversity of petroleum-polluted soil prior to the biostimulation process, and quantitative real-time PCR was used to determine changes in the bacterial community and functional genes (alkB, phnAc and nah) expressions throughout the biostimulation of petroleum-contaminated soil. The illumine results revealed that γ-proteobacteria, Chloroflexi, Firmicutes, and δ-proteobacteria were the most dominant bacterial phyla in the contaminated site, and that most of the strains were Gram-negative. The results of the gene expression results revealed that gram-negative bacteria and alkB are critical to successful bioremediation. Failure to maintain the stability of hydrocarbon-degrading bacteria and functional gene will reduce the extend to which alkanes and PAHs are degraded. According to the results of the study, the application of a C:N:P ratio of was 100:15:1 in the biodegradation experiment resulted in the highest rate at which petroleum hydrocarbons were biodegraded. The diversity of pollutant-degrading bacteria and the effective transfer of degrading genes among resident microorganisms are essential factors for the successful biostimulation of petroleum hydrocarbons. As such, screening these factors throughout the biostimulation process represents an effective monitoring approach by which the success of the biostimulation can be assessed.

Responses of microbial community from tropical pristine coastal soil to crude oil contamination

Brazilian offshore crude oil exploration has increased after the discovery of new reservoirs in the region known as pré-sal, in a depth of 7.000 m under the water surface. Oceanic islands near these areas represent sensitive environments, where changes in microbial communities due oil contamination could stand for the loss of metabolic functions, with catastrophic effects to the soil services provided from these locations. This work aimed to evaluate the effect of petroleum contamination on microbial community shifts (Archaea, Bacteria and Fungi) from Trindade Island coastal soils. Microcosms were assembled and divided in two treatments, control and contaminated (weathered crude oil at the concentration of 30 g kg(-1)), in triplicate. Soils were incubated for 38 days, with CO2 measurements every four hours. After incubation, the total DNA was extracted, purified and submitted for target sequencing of 16S rDNA, for Bacteria and Archaea domains and Fungal ITS1 region, using the Illumina MiSeq platform. Three days after contamination, the CO2 emission rate peaked at more than 20 × the control and the emissions remained higher during the whole incubation period. Microbial alpha-diversity was reduced for contaminated-samples. Fungal relative abundance of contaminated samples was reduced to almost 40% of the total observed species. Taxonomy comparisons showed rise of the Actinobacteria phylum, shifts in several Proteobacteria classes and reduction of the Archaea class Nitrososphaerales. This is the first effort in acquiring knowledge concerning the effect of crude oil contamination in soils of a Brazilian oceanic island. This information is important to guide any future bioremediation strategy that can be required.

The Biodiversity Changes in the Microbial Population of Soils Contaminated with Crude Oil

Crude oil spills resulting from excavation, transportation and downstream processes can cause intensive damage to living organisms and result in changes in the microbial population of that environment. In this study, we used a pyrosequencing analysis to investigate changes in the microbial population of soils contaminated with crude oil. Crude oil contamination in soil resulted in the creation of a more homogenous population of microorganisms dominated by members of the Actinomycetales, Clostridiales and Bacillales (all belonging to Gram-positive bacteria) as well as Flavobacteriales, Pseudomonadales, Burkholderiales, Rhizobiales and Sphingomonadales (all belonging to Gram-negative bacteria). These changes in the biodiversity decreased the ratios of chemoheterotrophic bacteria at higher concentrations of crude oil contamination, with these being replaced by photoheterotrophic bacteria, mainly Rhodospirillales. Several of the dominant microbial orders in the crude oil contaminated soils are able to degrade crude oil hydrocarbons and therefore are potentially useful for remediation of crude oil in contaminated sites.

From Rare to Dominant: a Fine-Tuned Soil Bacterial Bloom during Petroleum Hydrocarbon Bioremediation

Hydrocarbons are worldwide-distributed pollutants that disturb various ecosystems. The aim of this study was to characterize the short-lapse dynamics of soil microbial communities in response to hydrocarbon pollution and different bioremediation treatments. Replicate diesel-spiked soil microcosms were inoculated with either a defined bacterial consortium or a hydrocarbonoclastic bacterial enrichment and incubated for 12 weeks. The microbial community dynamics was followed weekly in microcosms using Illumina 16S rRNA gene sequencing. Both the bacterial consortium and enrichment enhanced hydrocarbon degradation in diesel-polluted soils. A pronounced and rapid bloom of a native gammaproteobacterium was observed in all diesel-polluted soils. A unique operational taxonomic unit (OTU) related to the Alkanindiges genus represented ∼ 0.1% of the sequences in the original community but surprisingly reached >60% after 6 weeks. Despite this Alkanindiges-related bloom, inoculated strains were maintained in the community and may explain the differences in hydrocarbon degradation. This study shows the detailed dynamics of a soil bacterial bloom in response to hydrocarbon pollution, resembling microbial blooms observed in marine environments. Rare community members presumably act as a reservoir of ecological functions in high-diversity environments, such as soils. This rare-to-dominant bacterial shift illustrates the potential role of a rare biosphere facing drastic environmental disturbances. Additionally, it supports the concept of "conditionally rare taxa," in which rareness is a temporary state conditioned by environmental constraints.

The coffee-machine bacteriome: biodiversity and colonisation of the wasted coffee tray leach

Microbial communities are ubiquitous in both natural and artificial environments. However, microbial diversity is usually reduced under strong selection pressures, such as those present in habitats rich in recalcitrant or toxic compounds displaying antimicrobial properties. Caffeine is a natural alkaloid present in coffee, tea and soft drinks with well-known antibacterial properties. Here we present the first systematic analysis of coffee machine-associated bacteria. We sampled the coffee waste reservoir of ten different Nespresso machines and conducted a dynamic monitoring of the colonization process in a new machine. Our results reveal the existence of a varied bacterial community in all the machines sampled, and a rapid colonisation process of the coffee leach. The community developed from a pioneering pool of enterobacteria and other opportunistic taxa to a mature but still highly variable microbiome rich in coffee-adapted bacteria. The bacterial communities described here, for the first time, are potential drivers of biotechnologically relevant processes including decaffeination and bioremediation.

Occurrence of Pseudomonas aeruginosa in Kuwait soil

Environmentally ubiquitous bacteria such as Pseudomonas aeruginosa evolved mechanisms to adapt and prevail under diverse conditions. In the current investigation, strains of P. aeruginosa demonstrating high rates of crude oil utilization and tolerance to high concentrations of heavy metals were found in both crude oil-contaminated and uncontaminated sites in Kuwait, and were dominant in the contaminated sites. The incidence of P. aeruginosa in tested soils implies the definitive pattern of crude oil contamination in the selection of the bacterial population in petroleum-contaminated sites in Kuwait. Surprisingly, the unculturable P. aeruginosa in different soil samples showed significant high similarity coefficients based on 16S-RFLP analyses, implying that the unculturable fraction of existing bacterial population in environmental samples is more stable and, hence, reliable for phylogenetic studies compared to the culturable bacteria.