The phyllosphere indigenous microbiota of Brassica campestris L. change its diversity in responding to di-n-butyl phthalate pollution

Effects of antibiotics on the endophyte and phyllosphere bacterial communities of lotus from above and below surface water in a typical shallow lake

Antibiotics are ubiquitous pollutants that are widely found in aquatic ecosystems, where the bacterial community of aquatic plants is influenced by antibiotics. However, differences between endophyte and phyllosphere bacteria of Lotus from above and below surface water remains unclear. Lotus samples from above and below the surface water were collected to investigate the differences in endophyte and phyllosphere bacteria and dominant environmental factors in regions with low (L-) and high (H-) total antibiotic levels. There were significant differences in Shannon diversity between endophyte and phyllosphere bacteria except between the below-surface water phyllosphere bacteria and below-surface water endophytes in both L-antibiotic and H-antibiotic regions, with higher values for phyllosphere bacteria. The dominant phylum in all phyllosphere samples was Proteobacteria (76.1%-92.5%), while Cyanobacteria (47.8%-81.1%) was dominant in all endophyte samples. The dominant source of above-surface water endophytes was below-surface water endophytes (83.68-91.25%), below-surface water phyllosphere bacteria (48.43-55.91%) for above-surface water phyllosphere bacteria, and above-surface water endophytes (53.83-61.80%) for below-surface water endophytes, while the dominant contributor to the below-surface water phyllosphere bacteria was also below-surface water endophytes (52.96-61.00%) in two regions, indicating that antibiotic stress changed the sink‒source relationship between endophytes and phyllosphere bacteria. The physical-chemical properties of surface water and sediments could be responsible for the variations in the above- and below-surface water endophytes and phyllosphere bacteria in both regions. It is suggested that antibiotics may have a substantial effect on endophyte and phyllosphere bacterial community.

Plant -microbe assisted emerging contaminants (ECs) removal and carbon cycling

Continuous increase in the level of atmospheric CO₂ and environmental contaminates has aggravated various threats resulting from environmental pollution and climate change. Research into plant -microbe interaction has been a central concern of ecology for over the year. However, despite the clear contribution of plant -microbe to the global carbon cycle, the role of plant -microbe interaction in carbon pools, fluxes and emerging contaminants (ECs) removal are still a poorly understood. The use of plant and microbes in ECs removal and carbon cycling is an attractive strategy because microbes operate as biocatalysts to remove contaminants and plant roots offer a rich niche for their growth and carbon cycling. However, bio-mitigation of CO₂ and removal of ECs is still under research phase because of the CO₂ capture and fixation efficiency is too low for industrial purposes and cutting-edge removal methods have not been created for such emerging contaminants.

Phyllosphere bacterial communities in urban green areas throughout Europe relate to urban intensity

The phyllosphere harbours a diverse and specific bacterial community, which influences plant health and ecosystem functioning. In this study, we investigated the impact of urban green areas connectivity and size on the composition and diversity of phyllosphere bacterial communities. Hereto, we evaluated the diversity and composition of phyllosphere bacterial communities of 233 Platanus x acerifolia and Acer pseudoplatanus trees in 77 urban green areas throughout 6 European cities. The community composition and diversity significantly differed between cities but only to a limited extent between tree species. We could show that urban intensity correlated significantly with the community composition of phyllosphere bacteria. In particular, a significant correlation was found between the relative abundances for 29 out of the 50 most abundant families and the urban intensity: the abundances of classic phyllosphere families, such as Acetobacteraceae, Planctomycetes, and Beijerinkiaceae, decreased with urban intensity (i.e. more abundant in areas with more green, lower air pollution, and lower temperature), while those related to human activities, such as Enterobacteriaceae and Bacillaceae, increased with urban intensity. The results of this study suggest that phyllosphere bacterial communities in European cities are associated with urban intensity and that effect is mediated by several combined stress factors.

Bacteria-driven phthalic acid ester biodegradation: Current status and emerging opportunities

The extensive use of phthalic acid esters (PAEs) has led to their widespread distribution across various environments. As PAEs pose significant threats to human health, it is urgent to develop efficient strategies to eliminate them from environments. Bacteria-driven PAE biodegradation has been considered as an inexpensive yet effective strategy to restore the contaminated environments. Despite great advances in bacterial culturing and sequencing, the inherent complexity of indigenous microbial community hinders us to mechanistically understand in situ PAE biodegradation and efficiently harness the degrading power of bacteria. The synthetic microbial ecology provides us a simple and controllable model system to address this problem. In this review, we focus on the current progress of PAE biodegradation mediated by bacterial isolates and indigenous bacterial communities, and discuss the prospective of synthetic PAE-degrading bacterial communities in PAE biodegradation research. It is anticipated that the theories and approaches of synthetic microbial ecology will revolutionize the study of bacteria-driven PAE biodegradation and provide novel insights for developing effective bioremediation solutions.

Isolation Chip Increases Culturable Bacterial Diversity and Reduces Cultivation Bias

Conventional cultivation methods, including petri dish plating, are selective and biased to enrich specific microorganisms, such as big population and fast-growing bacteria. In this study, we evaluated the ability of isolation chip (ichip) to reduce cultivation bias. We used the ichip and petri dish plating methods to cultivate bacteria from soil contaminated with (contaminated soil) or without (natural soil) crude oil. Ichip improved the richness and evenness of bacterial isolates in both the natural and contaminated soil samples. Using the petri dish plating method, Pseudomonas and Lysinibacillus isolates were found to be the most abundant, with over 50% of the relative abundance in the natural and oil-polluted soil-cultured communities, respectively. In comparison, using the ichip method, the isolates with the highest relative abundances were from Bacillus and Aeromonas in natural and contaminated soil-cultured communities, which only accounted for 20% and 28% of the total isolates, respectively. Interestingly, the evenness and richness of the bacteria varied slightly between the natural and oil-polluted soil samples, indicating that ichip had the ability to reduce the cultivation bias. In addition, oil selective pressure enriched the functional bacteria isolated using the petri dish plating method. In summary, ichip allows bacteria to grow evenly, as well as allowing for substance exchange between the environment and single cells. As such, it is a very good method for increasing culturable bacterial diversity and reducing cultivation bias.

Exploration of Intrinsic Microbial Community Modulators in the Rice Endosphere Indicates a Key Role of Distinct Bacterial Taxa Across Different Cultivars

Microbial communities associated with the plant phyllosphere and endosphere can have both beneficial as well as detrimental effects on their hosts. There is an ongoing debate to which extend the phyllosphere and endosphere microbiome assembly is controlled by the host plant how pronounced cultivar effects are. We investigated the bacterial and fungal communities from the phyllosphere and endosphere of 10 different rice cultivars grown under identical environmental conditions in the frame of a targeted approach to identify drivers of community assembly. The results indicated that the endophytic bacterial communities were clearly separated into two groups. The α-diversity and microbial network complexity within Group I were significantly lower than in Group II. Moreover, the genera Nocardioides, Microvirga, and Gaiella were significantly more abundant in Group II and only present in the interaction networks of this group. These three genera were significantly correlated with α- and β-diversity of the endophytic bacterial community and thus identified as major drivers of the endosphere community. We have identified keystone taxa that shape endophytic bacterial communities of different rice cultivars. Our overall findings provide new insights into plant-microbe interactions, and may contribute to targeted improvements of rice varieties in the future.

A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome

The plant leaf surface, or phyllosphere, represents a unique and challenging microbial biome with a diverse and dynamic community of commensal, parasitic, and mutualistic agents of microscopic proportions. This mini-review offers a digest of recently published research dedicated to the study of phyllosphere microbiota, framed in the context of processes and outcomes of microbial community assembly, structure, and (inter)activity in the phyllosphere, with particular focus on the contributions of environment, plant, and microbe, and on the potential benefits of interrogating those contributions at finer resolutions.

Phthalate Ester Contamination in Intensively Managed Greenhouse Facilities and the Assessment of Carcinogenic and Non-Carcinogenic Risk: A Regional Study

The contamination status and the potential carcinogenic and non-carcinogenic health risks from six phthalate esters (PAEs), nominated as priority pollutants by the United States Environmental Protection Agency (USEPA), were investigated in 40 typical greenhouses in three large-scale intensive greenhouse production areas in Jingmen city, Hubei province, central China. The total concentrations of PAEs in 40 soil samples and 80 vegetable samples ranged from 919 ± 134 to 7015 ± 475 µg kg⁻¹ (dry weight, DW), and from 387 ± 63, to 11,683 ± 1313 µg kg⁻¹ (DW), respectively. No carcinogenic risk was detected. The heat-map of the hazard quotient (HQ) values indicates the non-carcinogenic risks to children from di-n-butyl phthalate (DBP), at two sampling sites out of the 40, and from diethylhexyl phthalate (DEHP) (20 to young children and three to older children and adults) at 23 of the sites. The contamination risk from PAEs at Pengdun is of concern because only two of the 14 sampling sites selected there showed the non-carcinogenic risk to humans was unclear. The results of this study help to close a long-term knowledge gap resulting from a shortage of experimental data on PAE contamination in intensive greenhouse vegetable production in central China. The inclusion of DEHP in the Chinese list of priority pollutants is recommended, due to its increasing contamination and risk. This study provides valuable information for protected agricultural soil management and risk avoidance. It is a timely reminder to take PAE contamination and associated health risks into consideration, during the planning and introduction of intensively-managed greenhouse production systems.