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.

A novel actinomycete, strain 1_25(T), was isolated from soil under a black Gobi rock sample from Shuangta, PR China, and characterized using a polyphasic taxonomic approach. The results of comparative analysis of the 16S rRNA gene sequences indicated the 1_25(T) represented a member of the genus Streptomyces. Chemotaxonomic data revealed that 1_25(T) possessed MK-9(H-8) as the major menaquinone. The cell wall contained LL-diaminopimelic acid (LL-DAP) and the whole-cell sugar pattern consisted of ribose, glucose and galactose. Major fatty acid methyl esters were observed to be iso-C-16:0 (23.6%), and anteiso-C-15:0 (10.4%). The genomic DNA G+C content of 1_25(T) was 69 mol%. The results of phylogenetic analysis based on 16S rRNA gene sequence indicated that 1_25(T) had high sequence similarity with Streptomyces qinglanensis 172205(T) (98.1%), Streptomyces lycii TRM 66187(T) (98 %), and Streptomyces griseocarneus JCM4580(T) (98 %). In addition to the differences in phenotypic characters, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between 1_25(T) and closely related species were below the recommended threshold values for assigning strains to the same species. The fermentation product of 1_25(T) in ISP2 had an inhibitory effect on Staphylococcus aureus. On the basis of these genotypic and phenotypic characteristics, strain 1_25(T) (=JCM 34936(T)=GDMCC 4.216(T)) represents a novel species of the genus Streptomyces, for which the name Streptomyces gobiensis sp. nov. is proposed.

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.

Background The bacterial mechanisms responsible for hydrogen peroxide (H2O2) scavenging have been well-reported, yet little is known about how bacteria isolated from cold-environments respond to H2O2 stress. Therefore, we investigated the transcriptional profiling of the Planomicrobium strain AX6 strain isolated from the cold-desert ecosystem in the Qaidam Basin, Qinghai-Tibet Plateau, China, in response to H2O2 stress aiming to uncover the molecular mechanisms associated with H2O2 scavenging potential. Methods We investigated the H2O2-scavenging potential of the bacterial Planomicrobium strain AX6 isolated from the cold-desert ecosystem in the Qaidam Basin, Qinghai-Tibet Plateau, China. Furthermore, we used high-throughput RNA-sequencing to unravel the molecular aspects associated with the H2O2 scavenging potential of the Planomicrobium strain AX6 isolate. Results In total, 3,427 differentially expressed genes (DEGs) were identified in Planomicrobium strain AX6 isolate in response to 4 h of H2O2 (1.5 mM) exposure. Besides, Kyoto Encyclopedia of Genes and Genomes pathway and Gene Ontology analyses revealed the down- and/or up-regulated pathways following H2O2 treatment. Our study not only identified the H2O2 scavenging capability of the strain nevertheless also a range of mechanisms to cope with the toxic effect of H2O2 through genes involved in oxidative stress response. Compared to control, several genes coding for antioxidant proteins, including glutathione peroxidase (GSH-Px), Coproporphyrinogen III oxidase, and superoxide dismutase (SOD), were relatively up-regulated in Planomicrobium strain AX6, when exposed to H2O2. Conclusions Overall, the results suggest that the up-regulated genes responsible for antioxidant defense pathways serve as essential regulatory mechanisms for removing H2O2 in Planomicrobium strain AX6. The DEGs identified here could provide a competitive advantage for the existence of Planomicrobium strain AX6 in H2O2-polluted environments.

Pigments are an essential part of everyday life on Earth with rapidly growing industrial and biomedical applications. Synthetic pigments account for a major portion of these pigments that in turn have deleterious effects on public health and environment. Such drawbacks of synthetic pigments have shifted the trend to use natural pigments that are considered as the best alternative to synthetic pigments due to their significant properties. Natural pigments from microorganisms are of great interest due to their broader applications in the pharmaceutical, food, and textile industry with increasing demand among the consumers opting for natural pigments. To fulfill the market demand of natural pigments new sources should be explored. Cold-adapted bacteria and fungi in the cryosphere produce a variety of pigments as a protective strategy against ecological stresses such as low temperature, oxidative stresses, and ultraviolet radiation making them a potential source for natural pigment production. This review highlights the protective strategies and pigment production by cold-adapted bacteria and fungi, their industrial and biomedical applications, condition optimization for maximum pigment extraction as well as the challenges facing in the exploitation of cryospheric microorganisms for pigment extraction that hopefully will provide valuable information, direction, and progress in forthcoming studies.