Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial

From microbiome composition to functional engineering, one step at a time

SUMMARYCommunities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N+1/N-1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N-1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N-1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

Bioremediation of Oil-Contaminated Soil of the Republic of Kazakhstan Using a New Biopreparation

A new biopreparation is developed to clean soils from oil pollution in the arid climate of the Republic of Kazakhstan. The biopreparation includes bacterial strains R. qingshengii F2-1, R. qingshengii F2-2, and P. alloputida BS3701. When using the biopreparation in a liquid mineral medium with 15% crude oil, laboratory studies have revealed degradation of 48% n-alkanes and 39% of PAHs after 50 days. The effectiveness of the biopreparation has been demonstrated in field experiments in the soil contaminated with 10% crude oil at the K-Kurylys landfill, Republic of Kazakhstan. During the six-month field experiment, the number of oil degraders reached 10⁷ CFU/g soil, which degraded 70% of crude oil by the end of the experiment.

Effects of Soil Quality on the Microbial Community Structure of Poorly Evolved Mediterranean Soils

Physical and chemical alterations may affect the microbiota of soils as much as the specific presence of toxic pollutants. The relationship between the microbial diversity patterns and the soil quality in a Mediterranean context is studied here to test the hypothesis that soil microbiota is strongly affected by the level of anthropogenic soil alteration. Our aim has been to determine the potential effect of organic matter loss and associated changes in soil microbiota of poorly evolved Mediterranean soils (Leptosols and Regosols) suffering anthropogenic stress (i.e., cropping and deforestation). The studied soils correspond to nine different sites which differed in some features, such as the parent material, vegetation cover, or soil use and types. A methodological approach has been used that combines the classical physical and chemical study of soils with molecular characterization of the microbial assemblages using specific primers for Bacteria, Archaea and ectomycorrhizal Fungi. In agreement with previous studies within the region, physical, chemical and biological characteristics of soils varied notably depending on these factors. Microbial biomass, soil organic matter, and moisture, decreased in soils as deforestation increased, even in those partially degraded to substitution shrubland. Major differences were observed in the microbial community structure between the mollic and rendzic Leptosols found in forest soils, and the skeletic and dolomitic Leptosols in substitute shrublands, as well as with the skeletic and dolomitic Leptosols and calcaric Regosols in dry croplands. Forest soils displayed a higher microbial richness (OTU’s number) and biomass, as well as more stable and connected ecological networks. Here, we point out how human activities such as agriculture and other effects of deforestation led to changes in soil properties, thus affecting its quality driving changes in their microbial diversity and biomass patterns. Our findings demonstrate the potential risk that the replacement of forest areas may have in the conservation of the soil’s microbiota pool, both active and passive, which are basic for the maintenance of biogeochemical processes.

Impacts of Agriculture on the Environment and Soil Microbial Biodiversity

Agriculture represents an important mechanism in terms of reducing plant, animal, and microbial biodiversity and altering the environment. The pressure to cope with the increasing food demands of the human population has intensified the environmental impact, and alternative ways to produce food are required in order to minimize the decrease in biodiversity. Conventional agricultural practices, such as floods and irrigation systems; the removal of undesired vegetation by fires, tilling, and plowing; the use of herbicides, fertilizers, and pesticides; and the intensification of these practices over the last 50 years, have led to one of the most important environmental threats—a major loss of biodiversity. In this study, we review the impact that agriculture and its intensification have had on the environment and biodiversity since its invention. Moreover, we demonstrate how these impacts could be reduced through the use of microorganisms as biostimulants.

Fire alters plant microbiome assembly patterns: integrating the plant and soil microbial response to disturbance

It is increasingly evident that the plant microbiome is a strong determinant of plant health. While the ability to manipulate the microbiome in plants and ecosystems recovering from disturbance may be useful, our understanding of the plant microbiome in regenerating plant communities is currently limited. Using 16S ribosomal RNA (rRNA) gene and internal transcribed spacer (ITS) region amplicon sequencing, we characterized the leaf, stem, fine root, rhizome, and rhizosphere microbiome of < 1-yr-old aspen saplings and the associated bulk soil after a recent high-intensity prescribed fire across a burn severity gradient. Consistent with previous studies, we found that soil microbiomes are responsive to fire. We extend these findings by showing that certain plant tissue microbiomes also change in response to fire. Differences in soil microbiome compositions could be attributed to soil chemical characteristics, but, generally, plant tissue microbiomes were not related to plant tissue elemental concentrations. Using source tracking modeling, we also show that fire influences the relative dominance of microbial inoculum and the vertical inheritance of the sapling microbiome from the parent tree. Overall, our results demonstrate how fire impacts plant microbiome assembly, diversity, and composition and highlights potential for further research towards increasing plant fitness and ecosystem recovery after fire events.

The soil crisis: the need to treat as a global health problem and the pivotal role of microbes in prophylaxis and therapy

Soil provides a multitude of services that are essential to a healthily functioning biosphere and continuity of the human race, such as feeding the growing human population and the sequestration of carbon needed to counteract global warming. Healthy soil availability is the limiting parameter in the provision of a number of these services. As a result of anthropogenic abuses, and natural and global warming-promoted extreme weather events, Planet Earth is currently experiencing an unprecedented crisis of soil deterioration, desertification and erosive loss that increasingly prejudices the services it provides. Such services are pivotal to the Sustainability Development Goals formulated by the United Nations. Immediate and coordinated action on a global scale is urgently required to slow and ultimately reverse the loss of healthy soils. Despite the 'dirt-dust', non-vital appearance of soil, it is a highly dynamic living entity, whose life is overwhelmingly microbial. The soil microbiota, which constitutes the greatest reservoir and donor of microbial diversity on Earth, acts as a vast bioreactor, mediating a myriad of chemical reactions that turn the biogeochemical cycles, recycle wastes, purify water, and underpin the multitude of other services soil provides. Fuelling the belowground microbial bioreactor is the aboveground plant and photosynthetic surface microbial life which captures solar energy, fixes inorganic CO2 to organic carbon, and channels fixed carbon and energy into soil. In order to muster an effective response to the crisis, to avoid further deterioration, and to restore unhealthy soils, we need a new and coherent approach, namely to deal with soils worldwide as patients in need of health care and create (i) a public health system for development of effective policies for land use, conservation, restoration, recommendations of prophylactic measures, monitoring and identification of problems (epidemiology), organizing crisis responses, etc., and (ii) a healthcare system charged with soil care: the promotion of good practices, implementation of prophylaxis measures, and institution of therapies for treatment of unhealthy soils and restoration of drylands. These systems need to be national but there is also a desperate need for international coordination. To enable development of effective, evidence-based strategies that will underpin the efforts of soil healthcare systems, a substantial investment in wide-ranging interdisciplinary research on soil health and disease is mandatory. This must lead to a level of understanding of the soil:biota functionalities underlying key ecosystem services that enables formulation of effective diagnosis-prophylaxis-therapy pathways for sustainable use, protection and restoration of different types of soil resources in different climatic zones. These conservation-regenerative-restorative measures need to be complemented by an educative-political-economic-legislative framework that provides incentives encouraging soil care: knowledge, policy, economic and others, and laws which promote international adherence to the principles of restorative soil management. And: we must all be engaged in improving soil health; everyone has a duty of care (https://www.bbc.co.uk/ideas/videos/why-soil-is-one-of-the-most-amazing-things-on-eart/p090cf64). Creative application of microbes, microbiomes and microbial biotechnology will be central to the successful operation of the healthcare systems.

Mesocosm-based simulations to optimize a bioremediation strategy for the effective restoration of wildfire-impacted soils contaminated with high-molecular-weight hydrocarbons

AIMS

We obtained four microbial isolates from soil exposed to forest fire and evaluated their potential bioremediation activity when combined with a biosurfactant-producing bacterial strain for the decontamination of wildfire-impacted soil polluted with high-molecular-weight (HMW) hydrocarbons.

METHODS AND RESULTS

We established mesocosm trials to compare three bioremediation strategies: natural attenuation, bioaugmentation and biostimulation. Chemical analysis, culture-dependent and culture-independent methods were used to evaluate the bioremediation efficiency and speciation of the microbial cenoses based on these approaches. After treatment for 90 days, bioaugmentation removed 75·2-75·9% of the HMW hydrocarbons, biostimulation removed 63·2-69·5% and natural attenuation removed ~22·5%. Hydrocarbon degradation was significantly enhanced in the mesocosm supplemented with the biosurfactant-producing bacterial strain after 20 and 50 days of treatment compared to the other bioremediation strategies.

CONCLUSIONS

We found that the bioaugmentation approach was more effective than biostimulation and natural attenuation for the removal of HMW hydrocarbons from fire-impacted soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

Our study showed that micro-organisms from wildfire-impacted soil show significant potential for bioremediation, and that biosurfactant-producing bacterial strains can be combined with them as part of an effective bioremediation strategy.

Narrative of a versatile and adept species Pseudomonas putida

Pseudomonas putidais a fast-growing bacterium found mostly in temperate soil and water habitats. The metabolic versatility ofP. putidamakes this organism attractive for biotechnological applications such as biodegradation of environmental pollutants and synthesis of added-value chemicals (biocatalysis). This organism has been extensively studied in respect to various stress responses, mechanisms of genetic plasticity and transcriptional regulation of catabolic genes.P. putidais able to colonize the surface of living organisms, but is generally considered to be of low virulence. A number ofP. putidastrains are able to promote plant growth. The aim of this review is to give historical overview of the discovery of the speciesP. putidaand isolation and characterization ofP. putidastrains displaying potential for biotechnological applications. This review also discusses some major findings inP. putidaresearch encompassing regulation of catabolic operons, stress-tolerance mechanisms and mechanisms affecting evolvability of bacteria under conditions of environmental stress.

The versatility of Pseudomonas putida in the rhizosphere environment

This article addresses the lifestyle of Pseudomonas and focuses on how Pseudomonas putida can be used as a model system for biotechnological processes in agriculture, and in the removal of pollutants from soils. In this chapter we aim to show how a deep analysis using genetic information and experimental tests has helped to reveal insights into the lifestyle of Pseudomonads. Pseudomonas putida is a Plant Growth Promoting Rhizobacteria (PGPR) that establishes commensal relationships with plants. The interaction involves a series of functions encoded by core genes which favor nutrient mobilization, prevention of pathogen development and efficient niche colonization. Certain Pseudomonas putida strains harbor accessory genes that confer specific biodegradative properties and because these microorganisms can thrive on the roots of plants they can be exploited to remove pollutants via rhizoremediation, making the consortium plant/Pseudomonas a useful tool to combat pollution.

The Soil Microbiome of the Laurel Forest in Garajonay National Park (La Gomera, Canary Islands): Comparing Unburned and Burned Habitats after a Wildfire

The evergreen laurel forest is a relic of ancient subtropical/tropical forests, of which the best remnant in the Canary Islands is in Garajonay National Park, on La Gomera island. The soil microbiome associated with a mature undisturbed (unburned) laurel forest was characterized at two locations at different topographical positions on the mountain: The slope and the ridge crest. Given the unusual circumstance of an intense wildfire that severely affected part of this forest, the burned soils were also studied. The soil in undisturbed areas was relatively uniform. The bacterial community composition was dominated by bacteria from phyla Proteobacteria, Acidobacteria, and Actinobacteria. The wildfire changed the composition of the bacterial communities. The Acidobacteria, Actinobacteria, and Alphaproteobacteria (dominant class in unburned forests) significantly decreased in burned soils along with a parallel high increase in Betaproteobacteria, Bacteroidetes, and Firmicutes. We further showed the dramatic effect of a wildfire on the soil microbiome of the laurel forest, appearing as a loss of species richness and diversity, species dominance, and changes in the composition of the bacterial communities.

The burn severity and plant recovery relationship affect the biological and chemical soil properties of Pinus halepensis Mill. stands in the short and mid-terms after wildfire

In the Mediterranean Basin, changes in climate and fire regime (increased recurrence and severity) reduce ecosystem services after wildfires by increasing soil degradation and losses in plant diversity. Our study was a biological approach to relate soil properties to vegetation recovery and burn severity. We focused our study on the natural recovery of the soil-plant interphase in Pinus halepensis Mill. forests located in the SE of Iberian Peninsula, a semiarid climate. We included some chemical properties 3 years after fire (available phosphorus (P) and soil organic carbon (Corg), among others), and biological soil indicators 3 and 5 years after fire (i.e. basal soil respiration (BSR), microbial biomass carbon (Cmic), carbon mineralization coefficient (Cmineral), metabolic quotient (qCO₂) and microbial quotient (Cmic:Corg)). We analyzed the activity of three different enzymes: urease (UR), phosphatase (PHP) and β-glucosidase (GLU). The changes in most chemical properties were ephemeral, but P and Corg showed higher values in burned areas, and the highest were found for low-moderate severity. Plant recovery was the triggering factor for the recovery of Corg and biological soil function. Burn severity and time after fire influenced Cmic and the Cmic:Corg, which were higher for moderate-high severity 3 years later, but were below the unburned values 5 years after fire. The microbial activities of GLU and UR were recovered in burned areas 5 years after fire. The PHP values lowered according to higher burn severity and time after fire. The soil ecological trends obtained by a principal component analysis revealed a relationship linking GLU, BSR and qCO₂ that explained soil response to burn severity. PHP, Cmic and Cmic:Corg explained most of the variability related to time after fire. Our results provide insights into how burn severity, in Mediterranean fire-prone Aleppo pine stands, modulated the natural plant recovery linked to soil biochemical and microbiological response to fire. High burn severity limited natural vegetation recovery, and both reduced biological soil functionality. This knowledge can be implemented in post-fire planning to apply post-fire management (for mitigation and restoration) in which the "no intervention" tool should be contemplated. These findings provide information to be applied in adaptive forest management to improve the resilience of vulnerable ecosystems and to reduce burn severity in future fire events.

Emerging contaminants related to the occurrence of forest fires in the Spanish Mediterranean

Forest fires can be a source of contamination because, among others, of the use of chemicals to their extinction (flame retardants, FRs), or by the production of Polycyclic Aromatic Hydrocarbons (PAHs) derived from high temperature alteration of organic matter. Up to our knowledge, this study is the first to assess the direct (PAHs 16 on the USA EPA's priority list), and indirect [tri- to hepta- brominated diphenyl ethers (PBDEs), organophosphorus flame retardants (PFRs) and perfluoroalkyl substances (PFASs)] contamination related to forest fires. The abundance and distribution of these contaminants were monitored on two Mediterranean hillslopes, one burned and one unburned, near Azuébar (SE Spain). Samples were taken in the foot, middle, and top of the slope, at two depths, and in two environments (under canopy and bare soil). Sediments were collected from sediment fences after erosive rainfall events. Most of the screened compounds were found in both, burned and control hillslopes, though significant differences were found between both. In burned soil, low concentrations of PBDEs (maximum ΣPBDEs: 7.3ngg^-1), PFRs (664.4ngg^-1) and PFASs (56.4ngg^-1) were detected in relation to PAHs (Σ16 PAHs=1255.3ngg^-1). No significant influence of the hillslope position was observed for any of the contaminants but differences based on depth and vegetation presence tended to be significant, particularly for the PAHs. After the first erosive event, concentrations of PBDEs and PAHs were higher in sediment than in soil (ΣPBDEs: 17.8ngg^-1 and Σ16 PAHs=3154.2ngg^-1) pointing out the importance of connectivity processes, especially shortly after fire.

Metabolic Value Chemoattractants Are Preferentially Recognized at Broad Ligand Range Chemoreceptor of Pseudomonas putida KT2440

Bacteria have evolved a wide range of chemoreceptors with different ligand specificities. Typically, chemoreceptors bind ligands with elevated specificity and ligands serve as growth substrates. However, there is a chemoreceptor family that has a broad ligand specificity including many compounds that are not of metabolic value. To advance the understanding of this family, we have used the PcaY_PP (PP2643) chemoreceptor of Pseudomonas putida KT2440 as a model. Using Isothermal Titration Calorimetry we showed here that the recombinant ligand binding domain (LBD) of PcaY_PP recognizes 17 different C6-ring containing carboxylic acids with K_D values between 3.7 and 138 μM and chemoeffector affinity correlated with the magnitude of the chemotactic response. Mutation of the pcaY_PP gene abolished chemotaxis to these compounds; phenotype that was restored following gene complementation. Growth experiments using PcaY_PP ligands as sole C-sources revealed functional relationships between their metabolic potential and affinity for the chemoreceptor. Thus, only 7 PcaY_PP ligands supported growth and their K_D values correlated with the length of the bacterial lag phase. Furthermore, PcaY_PP ligands that did not support growth had significantly higher K_D values than those that did. The receptor has thus binds preferentially compounds that serve as C-sources and amongst them those that rapidly promote growth. Tightest binding compounds were quinate, shikimate, 3-dehydroshikimate and protocatechuate, which are at the interception of the biosynthetic shikimate and catabolic quinate pathways. Analytical ultracentrifugation studies showed that ligand free PcaY_PP-LBD is present in a monomer-dimer equilibrium (K_D = 57.5 μM). Ligand binding caused a complete shift to the dimeric state, which appears to be a general feature of four-helix bundle LBDs. This study indicates that the metabolic potential of compounds is an important parameter in the molecular recognition by broad ligand range chemoreceptors.

Bioaugmentation and biostimulation as strategies for the bioremediation of a burned woodland soil contaminated by toxic hydrocarbons: a comparative study

In this work, the natural attenuation strategy (no soil amendments done) was compared with two different bioremediation approaches, namely bioaugmentation through soil inoculation with a suspension of Trichoderma sp. mycelium and biostimulation by soil addition with a microbial growth promoting formulation, in order to verify the effectiveness of these methods in terms of degradation efficiency towards toxic hydrocarbons, with particular attention to the high molecular weight (HMW) fraction, in a forest area impacted by recent wildfire in Northern Italy. The area under investigation, divided into three parcels, was monitored to figure out the dynamics of decay in soil concentration of C₁₂₋₄₀ hydrocarbons (including isoalkanes, cycloalkanes, alkyl-benzenes and alkyl-naphthalenes besides PAHs) and low molecular weight (LMW) PAHs, following the adoption of the foregoing different remediation strategies. Soil hydrocarbonoclastic potential was even checked by characterizing the autochthonous microbial cenoses. Field experiments proved that the best performance in the abatement of HMW hydrocarbons was reached 60 days after soil treatment through the biostimulation protocol, when about 70% of the initial concentration of HMW hydrocarbons was depleted. Within the same time, about 55% degradation was obtained with the bioaugmentation protocol, whilst natural attenuation allowed only a 45% removal of the starting C12-40 hydrocarbon fraction. Therefore, biostimulation seems to significantly reduce the time required for the remediation, most likely because of the enhancement of microbial degradation through the improvement of nutrient balance in the burned soil.