Urban trees are crucial in delivering essential ecosystem services, including air pollution mitigation. This service is influenced by plant associated microbiomes, which can degrade hydrocarbons, support tree health, and influence ecological processes. Yet, our understanding of tree microbiomes remains limited, thus affecting our ability to assess and quantify the ecosystem services provided by trees as complex systems. The main hypothesis of this work was that tree microbiomes concur to hydrocarbon biodegradation, and was tested through three case studies, which collectively investigated two tree micro-habitats (phyllosphere and tree cavity organic soil-TCOS) under various conditions representing diverse ecological scenarios, by applying different culture-based and molecular techniques and at different scales. The integration of all results provided a more comprehensive understanding of the role of microbiomes in urban trees. Firstly, bacterial strains isolated from the phyllosphere of Quercus ilex were characterized, indicating the presence of Plant-Growth Promoting bacteria and strains able to catabolize PAHs, particularly naphthalene and phenanthrene. Secondly, naphthalene biodegradation on artificially spiked Hedera helix leaves was quantified in greenhouse experiments on inoculated and untreated plants. The persistence of the inoculated strain and community structure of epiphytic bacteria were assessed by Illumina sequencing of V5-V6 hypervariable regions of 16S rRNA gene. Results showed that naphthalene degradation was initially faster on inoculated plants but later the degradation rates became similar, probably because bacterial populations with hydrocarbon-degrading abilities gradually developed also on non-inoculated plants. Finally, we explored bacterial and fungal biodiversity hosted by TCOS samples, collected from six large trees located in an urban park and belonging to different species. Microbial communities were characterized by Illumina sequencing of V5-V6 hypervariable regions of bacterial gene 16S rRNA and of fungal ITS1. Results indicated TCOS as a distinct substrate, whose microbiome is determined both by the host tree and by canopy environmental conditions and has a pronounced aerobic hydrocarbon degradation potential. Overall, a better assessment of biodiversity associated with trees and the subsequent provision of ecosystem services constitute a first step toward developing future new microbe-driven sustainable solutions, especially in terms of support for urban green planning and management policy.

• Klíčová slova
• air pollution mitigation, ecosystem services, hydrocarbon biodegradation, phyllosphere, tree cavity organic soil, tree-related microhabitats, urban trees,
• Publikační typ
• časopisecké články MeSH

Finding solutions for the remediation and restoration of abandoned mining areas is of great environmental importance as they pose a risk to ecosystem health. In this study, our aim was to determine how remediation strategies with (i) compost amendment, (ii) planting a metal-tolerant grass Bouteloua curtipendula, and (iii) its inoculation with beneficial endophytes influenced the microbiome of metal-contaminated tailings originating from the abandoned Blue Nose Mine, SE Arizona, near Patagonia (USA). We conducted an indoor microcosm experiment followed by a metataxonomic analysis of the mine tailings, compost, and root samples. Our results showed that each remediation strategy promoted a distinct pattern of microbial community structure in the mine tailings, which correlated with changes in their chemical properties. The combination of compost amendment and endophyte inoculation led to the highest prokaryotic diversity and total nitrogen and organic carbon, but also induced shifts in microbial community structure that significantly correlated with an enhanced potential for mobilization of Cu and Sb. Our findings show that soil health metrics (total nitrogen, organic carbon and pH) improved, and microbial community changed, due to organic matter input and endophyte inoculation, which enhanced metal leaching from the mine waste and potentially increased environmental risks posed by Cu and Sb. We further emphasize that because the initial choice of remediation strategy can significantly impact trace element mobility via modulation of both soil chemistry and microbial communities, site specific, bench-scale preliminary tests, as reported here, can help determine the potential risk of a chosen strategy.

• Klíčová slova
• Compost, Endophyte, Microbial communities, Mine tailings, Restoration, Trace elements,
• Publikační typ
• časopisecké články MeSH

Phytoremediation of petroleum hydrocarbons in subarctic regions relies on the successful establishment of plants that stimulate petroleum-degrading microorganisms, which can be challenging due to the extreme climate, limited nutrients, and difficulties in maintaining sites in remote locations. A long-term phytoremediation experiment was initiated in Alaska in 1995 with the introduction of grasses and/or fertilizer to petroleum hydrocarbon (PHC)-contaminated soils that were subsequently left unmanaged. In 2011, the PHC concentrations were below detection limits in all soils tested and the originally planted grasses had been replaced by volunteer plant species that had colonized the site. Here, we sought to understand how the original treatments influenced the structure of prokaryotic communities associated with plant species that colonized the soils and to assess the interactions between the rhizospheric and endophytic communities of the colonizing vegetation 20 years after the experiment was established. Metataxonomic analysis performed using 16S rRNA gene sequencing revealed that the original type of contaminated soil and phytoremediation strategy influenced the structure of both rhizospheric and endophytic communities of colonizing plants, even 20 years after the treatments were applied and following the disappearance of the originally planted grasses. Our findings demonstrate that the choice of initial phytoremediation strategy drove the succession of microorganisms associated with the colonizing vegetation. The outcome of this study provides new insight into the establishment of plant-associated microbial communities during secondary succession of subarctic areas previously contaminated by PHCs and indicates that the strategies for restoring these ecosystems influence the plant-associated microbiota in the long term. IMPORTANCE Subarctic ecosystems provide key services to local communities, yet they are threatened by pollution caused by spills and disposal of petroleum waste. Finding solutions for the remediation and restoration of subarctic soils is valuable for reasons related to human and ecosystem health, as well as environmental justice. This study provides novel insight into the long-term succession of soil and plant-associated microbiota in subarctic soils that had been historically contaminated with different sources of PHCs and subjected to distinct phytoremediation strategies. We provide evidence that even after the successful removal of PHCs and the occurrence of secondary succession, the fingerprint of the original source of contamination and the initial choice of remediation strategy can be detected as a microbial legacy in the rhizosphere, roots, and shoots of volunteer vegetation even 2 decades after the contamination had occurred. Such information needs to be borne in mind when designing and applying restoration approaches for PHC-contaminated soils in subarctic ecosystems.

• Klíčová slova
• bacterial communities, endophyte, petroleum hydrocarbons, phytoremediation, rhizosphere, rhizosphere-inhabiting microbes, secondary succession, subarctic,
• Publikační typ
• časopisecké články MeSH

In terms of the number and diversity of living units, the prokaryotic empire is the most represented form of life on Earth, and yet it is still to a significant degree shrouded in darkness. This microbial "dark matter" hides a great deal of potential in terms of phylogenetically or metabolically diverse microorganisms, and thus it is important to acquire them in pure culture. However, do we know what microorganisms really need for their growth, and what the obstacles are to the cultivation of previously unidentified taxa? Here we review common and sometimes unexpected requirements of environmental microorganisms, especially soil-harbored bacteria, needed for their replication and cultivation. These requirements include resuscitation stimuli, physical and chemical factors aiding cultivation, growth factors, and co-cultivation in a laboratory and natural microbial neighborhood.

• Klíčová slova
• VBNC, cultivation techniques, difficult-to-culture microorganisms, dormancy, environmental microbiome, growth factors, improved cultivation, microbial ecology,
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH

BACKGROUND: Although fertilization and crop rotation practices are commonly used worldwide in agriculture to maximize crop yields, their long-term effect on the structures of soil microorganisms is still poorly understood. This study investigated the long-term impact of fertilization and crop rotation on soil microbial diversity and the microbial community structure in four different locations with three soil types. Since 1996, manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and NPK (NPK; 330 kg N/ha) fertilizers were periodically applied to the soils classified as chernozem, luvisol and cambisol, which are among the most abundant or fertile soils used for agricultural purposes in the world. In these soils, potato (Solanum tuberosum L.), winter wheat (Triticum aestivum L.), and spring barley (Hordeum vulgare L.) were rotated every three years. RESULTS: Soil chemistry, which was significantly associated with location, fertilization, crop rotation, and the interaction of fertilization and location, was the dominant driver of soil microbial communities, both prokaryotic and fungal. A direct effect of long-term crop rotation and fertilization on the structure of their communities was confirmed, although there was no evidence of their influence on microbial diversity. Fungal and bacterial communities responded differently to fertilization treatments; prokaryotic communities were only significantly different from the control soil (CF) in soils treated with MF and SF3x, while fungal communities differed across all treatments. Indicator genera were identified for different treatments. These taxa were either specific for their decomposition activities or fungal plant pathogens. Sequential rotation of the three crops restricted the growth of several of the indicator plant pathogens. CONCLUSIONS: Long-term fertilization and crop rotation significantly altered microbial community structure in the soil. While fertilization affected soil microorganisms mainly through changes in nutrient profile, crop rotations lead to the attraction and repulsion of specific plant pathogens. Such changes in soil microbial communities need to be considered when planning soil management.

• Klíčová slova
• Cambisol, Chernozem, Community structure, Luvisol, Manure, Microbial diversity, NPK fertilizers, Sewage sludge,
• Publikační typ
• časopisecké články MeSH

An understanding of how fertilization influences endophytes is crucial for sustainable agriculture, since the manipulation of the plant microbiome could affect plant fitness and productivity. This study was focused on the response of microbial communities in the soil and tubers to the regular application of manure (MF; 330 kg N/ha), sewage sludge (SF; 330 and SF3x; 990 kg N/ha), and chemical fertilizer (NPK; 330-90-300 kg N-P-K/ha). Unfertilized soil was used as a control (CF), and the experiment was set up at two distinct sites. All fertilization treatments significantly altered the prokaryotic and fungal communities in soil, whereas the influence of fertilization on the community of endophytes differed for each site. At the site with cambisol, prokaryotic and fungal endophytes were significantly shifted by MF and SF3 treatments. At the site with chernozem, neither the prokaryotic nor fungal endophytic communities were significantly associated with fertilization treatments. Fertilization significantly increased the relative abundance of the plant-beneficial bacteria Stenotrophomonas, Sphingomonas and the arbuscular mycorrhizal fungi. In tubers, the relative abundance of Fusarium was lower in MF-treated soil compared to CF. Although fertilization treatments clearly influenced the soil and endophytic community structure, we did not find any indication of human pathogens being transmitted into tubers via organic fertilizers.

• Klíčová slova
• NPK, endophytic communities, manure, sewage sludge, soil microbial communities,
• Publikační typ
• časopisecké články MeSH