The damage caused by soil-borne diseases in Cunninghamia lanceolata (Lamb.) Hook (Cupressaceae), commonly called the Chinese fir, has become increasingly severe in China in recent years. Due to the strong seasonal dependence of the occurrence and severity of these diseases, the ecological processes influencing changes in the composition and function of the plant microbiome during different seasons of pathogen infection have been rarely studied. This study compared the seasonal variations in soil physicochemical properties between the rhizosphere soils of healthy and diseased C. lanceolata in major production areas in China. It further explored the effects of root rot on the composition, structure, and ecological functions of rhizosphere microorganisms. The results demonstrated that seasonal variations significantly influenced the physicochemical properties and microbial composition of the rhizosphere soil in C. lanceolata affected by root rot. Microbiome analysis further confirmed that, within the same season, healthy C. lanceolata contained a greater abundance of ecologically beneficial microbial taxa in the rhizosphere soil compared to diseased trees. These microorganisms may function as bioprotectants. This study enhances our understanding of the structural and functional changes in the rhizosphere soil microbiome associated with soil-borne diseases and provides potential ecological management strategies to improve plant resistance to root rot.

Numerous specimens stored in natural history collections have been involuntarily preserved together with their associated microbiomes. We propose exploiting century-old soils occasionally found on the roots of herbarium plants to assess the diversity of ancient soil microbial communities originally associated with these plants. We extracted total DNA and sequenced libraries produced from rhizospheric soils and roots of four plants preserved in herbaria for more than 120 years in order to characterise the preservation and taxonomic diversity that can be recovered in such contexts. Extracted DNA displayed typical features of ancient DNA, with cytosine deamination at the ends of fragments predominantly shorter than 50 bp. When compared to extant microbiomes, herbarium microbial communities clustered with soil communities and were distinct from communities from other environments. Herbarium communities also displayed biodiversity features and assembly rules typical of soil and plant-associated ones. Soil communities were richer than root-associated ones with which they shared most taxa. Regarding community turnover, we detected collection site, soil versus root and plant species effects. Eukaryotic taxa that displayed a higher abundance in roots were mostly plant pathogens that were not identified among soil-enriched ones. Conservation of these biodiversity features and assembly rules in herbarium-associated microbial communities indicates that herbarium-extracted DNA might reflect the composition of the original plant-associated microbial communities and that preservation in herbaria seemingly did not dramatically alter these characteristics. Using this approach, it should be possible to investigate historical soils and herbarium plant roots to explore the diversity and temporal dynamics of soil microbial communities.

Agriculture, including horticulture, can support and provide food for the global population, meeting both nutritional and economic needs. However, plant diseases induced by phytopathogens result in enormous losses in horticultural crop production through decreasing yields and the quality of crops. Notably, fungal phytopathogens are responsible for over 40% of these diseases. Among them, Fusarium represents a significant group of pathogenic fungi that inflict damage and reduce crop yields, thereby contributing to declines in food supplies. Conventional approaches to addressing these issues involve methods such as intercropping, crop rotation, soil solarization, and the use of synthetic fungicides. However, these methods may cause environmental problems, increase disease resistance, and result in the emergence of new pathogens with elevated resistance levels. Furthermore, the use of gene editing technology to prevent Fusarium diseases faces regulatory approval challenges and health risks. Biological control is recognized as an efficient strategy for managing a wide array of plant diseases by employing bacteria and fungi as agents to combat phytopathogens. Trichoderma is a widely recognized fungal genus employed as a biological control agent, with the potential to be a commercial biological control agent to suppress the growth of Fusarium. This article explores Trichoderma's role in managing Fusarium-related diseases in horticultural crops, highlighting its potential as a biocontrol agent and the challenges in scaling up its utilization.

Twenty-three species of the genera Aspistomella Hendel, 1909, Polyteloptera Hendel, 1909, and Ulivellia Speiser, 1929 occurring in South America (Colombia, Peru, Bolivia, and Brazil) form a monophyletic lineage sharing certain combinations of plesiomorphies and apomorphies with similar larval biology. The name Aspistomella Hendel, 1909 is a new senior subjective synonym of Paraphyola Hendel, 1909. The group of genera is extended by the addition of six known species, Aspistomella angustifrons (Hendel, 1909) comb. nov., A. crucifera (Hendel, 1909) comb. nov., A. lobioptera Hendel, 1909, A. heteroptera Hendel, 1909, A. lunata (Hendel, 1909) comb. nov., Polyteloptera apotropa Hendel, 1909, and Ulivellia inversa Speiser, 1929, and 17 previously unknown species. Aspistomella duo Kovac, Kameneva & v. Korneyev, sp. nov., A. enderleini Kameneva & v. Korneyev, sp. nov., A. garleppi Kameneva & v. Korneyev, sp. nov., A. obliqua Kameneva, v. Korneyev & Savaris, sp. nov., A. pachitea Kameneva & v. Korneyev, sp. nov., A. quinquincisa Kameneva & v. Korneyev, sp. nov., A. sachavaca Smit & Kameneva, sp. nov., A. schnusei Kameneva & v. Korneyev, sp. nov., A. steyskali Kameneva & S. Korneyev, sp. nov., A. teresensis Ara & uacute;jo, v. Korneyev & Savaris, sp. nov., A. tres Kovac, Kameneva & v. Korneyev, sp. nov., Ulivellia amnoni Smit, sp. nov., U. arcuata Kovac & Kameneva, sp. nov., U. laetitiae Smit, sp. nov., U. pseudinsolita Kameneva & v. Korneyev sp. nov., and U. tenoris Kovac & Kameneva sp. nov. are described. A key to the genera and species is given. Among the Lipsanini, this group of genera is easily recognised by the combination of an enlarged, anteriorly produced epistome (lower part of the face) and a low clypeus (in the other lipsanine genera the clypeus is high and the epistome is not enlarged), which supports its monophyly, and the differentiated short parafrontal setulae and long and strong frontal and interfrontal setae, which is a synapomorphy of a larger monophyletic lineage that also includes Chaetopsis Loew, 1868 and related taxa, as well as Amethysa Macquart, 1835, Euphara Loew, 1868 and their relatives. As far as is known, most species of this larger lineage are associated with various Poaceae plants. The species included here in the Aspistomella group are also associated with neotropical tall grasses: bamboo ( Guadua ) and wild cane ( Gynerium ). Aspistomella and Ulivellia larvae inhabit water-filled internode cavities (= bamboo phytotelmata) of living bamboo culms of Guadua angustifolia. Newly emerged larvae use tunnels made by lepidopteran borers (Crambidae caterpillars) to penetrate the hard bamboo walls. Aspistomella and Ulivellia larvae are saprophagous and adapted to an aquatic lifestyle. The last instar larvae jump easily and pupate in the soil. The external morphology, cuticular sensilla and cephalopharyngeal skeletons of the third instar larvae of five Aspistomella and Ulivellia species (one with unknown adult stage) were studied by light and scanning electron microscopy. The main features that allow the identification of larvae and puparia are the unique posterior spiracles and the structure of the abdominal creeping welts. The morphological characteristics of Aspistomella and Ulivellia larvae are compared with other Lipsanini and their feeding habits with other ulidiids. An identification key for Aspistomella and Ulivellia is given. The adaptations to life in bamboo phytotelmata found in both neotropical Aspistomella and Ulivellia and in oriental members of the closely related family Tephritidae are discussed.

Phosphonates (PHTs), organic compounds with a stable C-P bond, are widely distributed in nature. Glyphosate (GP), a synthetic PHT, is extensively used in agriculture and has been linked to various human health issues and environmental damage. Given the prevalence of GP, developing cost-effective, on-site methods for GP detection is key for assessing pollution and reducing exposure risks. We adopted Agrobacterium tumefaciens CHLDO, a natural GP degrader, as a host and the source of genetic parts for constructing PHT biosensors. In this bacterial species, the phn gene cluster, encoding the C-P lyase pathway, is regulated by the PhnF transcriptional repressor. We selected the phnG promoter, which displays a dose-dependent response to GP, to build a set of whole-cell biosensors. Through stepwise genetic optimization of the transcriptional cascade, we created a whole-cell biosensor capable of detecting GP in the 0.25-50 mu M range in various samples, including soil and water.

Nickel oxide nanoparticles (NiO-NPs) are common nanomaterials that may be released into the environment, affecting the toxicity of other contaminants. Atrazine (ATZ) is a commonly used herbicide that can harm organisms due to its persistence and bioaccumulation in the environment. Although the toxicity of ATZ to earthworms is well-documented, the risk of co-exposure with NiO-NPs increases as more nanoparticles accumulate in the soil. In this study, we investigated the effects and mechanisms of NiO-NPs on the accumulation of ATZ in earthworms. The results showed that after day 21, the antioxidant system of the cells under ATZ treatment alone was adversely affected, with ROS content 36.05 % higher than that of the control (CK) group. However, the addition of NiO-NPs reduced the ROS contents in the earthworms by 0.6 %- 32.3 %. Moreover, analysis of earthworm intestinal sections indicates that NiO-NPs mitigated cellular and tissue damage caused by ATZ. High-throughput sequencing revealed that NiO-NPs in earthworm intestines increased the abundance of Pseudomonas aeruginosa and Aeromonas aeruginosa. Additionally, the enhanced function of the ABC transport system in the gut resulted in lower accumulation of ATZ in earthworms. In summary, NiO-NPs can reduce the accumulation and thus the toxicity of ATZ in earthworms. Our study contributes to a deeper understanding of the effects of NiO-NPs on co-existing pollutants.

The Qinghai-Tibet Plateau glaciers are an important carrier of mercury (Hg). With global warming, Hg enters into the downstream ecosystem in the melt waters, threatening human health and ecosystem security in the region. Methylmercury (MeHg), which has higher toxicity than Hg itself, is converted from inorganic Hg. However, little is known about the process of Hg methylation and, in particular, microbial Hg methylation in high altitude mountain glaciers. We combined Hg speciation measurements and metagenomic analysis of 6 sample types from the terminus of Laohugou No.12 glacier to elucidate potential microbially mediated Hg methylation. We found higher Hg concentrations in supraglacial cryoconite (SC) and dusty layer (DL) samples which contain considerable debris and dust. In addition, MeHg concentrations were highest in some of these SC and DL samples. Bacterial hgcA Hg methylation genes were present in all samples except supraglacial ice but were of highest abundance in SC and DL. This suggested that microbial Hg methylation is most likely to occur in SC and DL. There were 8 phyla of potential Hg methylation microorganisms, but 37% of the sequences could not be classified into any known genus. Most of the hgcA sequences were closely related to sequences from previously reported Hg methylating genera within the Deltaproteobacteria and Firmicutes, but the common Hg methylating Methanomicrobia were absent in glacial samples. (C) 2019 Elsevier B.V. All rights reserved.

A range of fungal species showed variable abilities to colonize and penetrate a mortar substrate. Calcium biomineralization was a common feature with calcium-containing crystals deposited in the microenvironment or encrusting hyphae, regardless of the specific mortar composition. Several species caused significant damage to the mortar surface, exhibiting burrowing and penetration, surface etching, and biomineralization. In some cases, extensive biomineralization of hyphae, probably by carbonatization, resulted in the formation of crystalline tubes after hyphal degradation on mortar blocks, including those amended with Co or Sr carbonate. Ca was the only metal detected in the biomineralized formations with Co or Sr undetectable. Aspergillus niger, Stemphylium sp. and Paecilomyces sp. could penetrate mortar with differential responses depending on the porosity. Fluorescent staining of thin sections recorded penetration depths of similar to 530 um for A. niger and similar to 620 um for Stemphylium sp. Penetration depth varied inversely with porosity and greater penetration depths were achieved in mortar with a lower porosity (lower water/cement ratio). These results have provided further understanding of biodeteriorative fungal interactions with cementitious substrates that can clearly affect structural integrity. The potential significance of fungal colonization and such biodeteriorative phenomena should not be overlooked in built environment contexts, including radionuclide storage and surface decontamination.

Climate change is rapidly transforming Arctic landscapes where increasing soil temperatures speed up permafrost thaw. This exposes large carbon stocks to microbial decomposition, possibly worsening climate change by releasing more greenhouse gases. Understanding how microbes break down soil carbon, especially under the anaerobic conditions of thawing permafrost, is important to determine future changes. Here, we studied the microbial community dynamics and soil carbon decomposition potential in permafrost and active layer soils under anaerobic laboratory conditions that simulated an Arctic summer thaw. The microbial and viral compositions in the samples were analyzed based on metagenomes, metagenome-assembled genomes, and metagenomic viral contigs (mVCs). Following the thawing of permafrost, there was a notable shift in microbial community structure, with fermentative Firmicutes and Bacteroidota taking over from Actinobacteria and Proteobacteria over the 60-day incubation period. The increase in iron and sulfate-reducing microbes had a significant role in limiting methane production from thawed permafrost, underscoring the competition within microbial communities. We explored the growth strategies of microbial communities and found that slow growth was the major strategy in both the active layer and permafrost. Our findings challenge the assumption that fast-growing microbes mainly respond to environmental changes like permafrost thaw. Instead, they indicate a common strategy of slow growth among microbial communities, likely due to the thermodynamic constraints of soil substrates and electron acceptors, and the need for microbes to adjust to post-thaw conditions. The mVCs harbored a wide range of auxiliary metabolic genes that may support cell protection from ice formation in virus-infected cells.IMPORTANCE As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change. As the Arctic warms, thawing permafrost unlocks carbon, potentially accelerating climate change by releasing greenhouse gases. Our research delves into the underlying biogeochemical processes likely mediated by the soil microbial community in response to the wet and anaerobic conditions, akin to an Arctic summer thaw. We observed a significant shift in the microbial community post-thaw, with fermentative bacteria like Firmicutes and Bacteroidota taking over and switching to different fermentation pathways. The dominance of iron and sulfate-reducing bacteria likely constrained methane production in the thawing permafrost. Slow-growing microbes outweighed fast-growing ones, even after thaw, upending the expectation that rapid microbial responses to dominate after permafrost thaws. This research highlights the nuanced and complex interactions within Arctic soil microbial communities and underscores the challenges in predicting microbial response to environmental change.

Soil pollution by TNT(2,4,6-trinitrotoluene), RDX(hexahydro-1,3,5-trinitro-1,3,5-triazacyclohexane), and HMX(octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine), resulting from the use of explosives, poses significant challenges, leading to adverse effects such as toxicity and alteration of microbial communities. Consequently, there is a growing need for effective bioremediation strategies to mitigate this damage. This review focuses on Microbial and Bio-omics perspectives within the realm of soil pollution caused by explosive compounds. A comprehensive analysis was conducted, reviewing 79 articles meeting bibliometric criteria from the Web of Science and Scopus databases from 2013 to 2023. Additionally, relevant patents were scrutinized to establish a comprehensive research database. The synthesis of these findings serves as a critical resource, enhancing our understanding of challenges such as toxicity, soil alterations, and microbial stress, as well as exploring bio-omics techniques like metagenomics, transcriptomics, and proteomics in the context of environmental remediation. The review underscores the importance of exploring various remediation approaches, including mycorrhiza remediation, phytoremediation, bioaugmentation, and biostimulation. Moreover, an examination of patented technologies reveals refined and efficient processes that integrate microorganisms and environmental engineering. Notably, China and the United States are pioneers in this field, based on previous successful bioremediation endeavors. This review underscores research's vital role in soil pollution via innovative, sustainable bioremediation for explosives.