Variations in the bacterial community compositions at different sites in the tomb of Emperor Yang of the Sui Dynasty

Trichoderma spp. promotes ginseng biomass by influencing the soil microbial community

Introduction

Ginseng (Panax ginseng C.A. Meyer) has multiple effects on human health; however, soil degradation seriously affects its yield. Trichoderma spp. play an important role in improving plant biomass by influencing the soil environment. Therefore, it is necessary to screen efficient Trichoderma strains that can increase ginseng biomass and determine their mechanisms.

Methods

Herein, we selected six Trichoderma species (T. brevicompactum, T. velutinum, T. viridescens, T. atroviride, T. koningiopsis, and T. saturnisporum) isolated from ginseng rhizosphere soil, and evaluated their growth promoting effects on ginseng and their influence on the microbiome and chemical attributes of the ginseng rhizosphere soil.

Results

Except for T. saturnisporum (F), compared with the control, the other five species increased ginseng biomass. In terms of chemical properties, the pH value, available potassium content, and available phosphorus content in the ginseng rhizosphere soil increased by 1.16-5.85%, 0.16-14.03%, and 3.92-38.64%, respectively, after root irrigation with spores of Trichoderma species. For the soil microbiome, fungal Chao1 and Ace richness indices decreased. Application of Trichoderma enhanced the relative level of Proteobacteria, but reduced the relative level of Ascomycota. At the genus level, application of Trichoderma enhanced the relative levels of Sphingomonas, Blastomonas, and Trichoderma, but reduced the relative level of Fusarium. Available K and available P were the most important elements that affected the structure of the bacterial community, while total K was the most influential element for the structure of the fungal community structure.

Conclusion

The results indicated that the application of Trichoderma spp. could increase soil nutrients and regulate the structure and composition of the soil microbial community, thereby enhancing the biomass of ginseng. The results will provide guidance for soil improvement in ginseng cultivation.

Differences of airborne and mural microorganisms in a 1,500-year-old Xu Xianxiu's Tomb, Taiyuan, China

Background

Microbial colonization represents one of the main threats to the conservation of subterranean cultural heritage sites. Recently, the microbial colonization on murals in tombs has gradually attracted attention.

Methods

In this study, a total of 33 samples, including 27 aerosol samples and 6 mural painting samples, were collected from different sites of Xu Xianxiu's Tomb and analyzed using culture-dependent methods. We compared the diversities of culturable bacteria and fungi isolated from the air and murals and explored the potential impacts of microorganisms on the biodeterioration of the murals.

Results

Phylogenetic analyses revealed that the culturable bacteria belonged to Bacillus, Microbacterium, Lysobacter and Arthrobacter. And the most of fungal belonged to the Penicillium, Cladosporium and Aspergillus genera. The composition and structure of airborne bacteria and fungi outside the tomb were both significantly different from that inside the tomb. The variation trends of airborne bacterial and fungal concentrations at different sampling sites were remarkably similar. Bacillus frigoritolerans, Bacillus halotolerans, Bacillus safensis, Exiguobacterium mexicanum, Microbacterium trichothecenolyticum, and Micrococcus yunnanensis were bacterial species commonly isolated from both the mural and air environments. Fungal species commonly isolated from aerosol samples and mural painting samples were Alternaria alternata, Cladosporium cladosporioides, Penicillium brevicompactum, and Peyronellaea glomerata. The prediction of the ecological functions of the bacteria revealed that chemoheterotrophy or aerobic_chemoheterotrophy accounted for substantial relative proportions in all sample types.

Conclusion

These results suggest that the aerosol circulation between the inside and outside environments of the tomb was weak and that the outside environment had yet to have an impact on the air microbial community inside the tomb. Selective colonization of microorganisms, which is mediated by interaction between microorganisms and special microenvironmental factors, is an important reason for the biodeterioration of murals.

Comparative assessment of soil microbial community in crude oil contaminated sites

Petroleum refineries generate oily sludge that contains hazardous polycyclic aromatic hydrocarbons (PAH), and hence, its proper disposal is of foremost concern. Analysis of the physicochemical properties and functions of indigenous microbes of the contaminated sites are essential in deciding the strategy for bioremediation. This study analyses both parameters at two geographically distant sites, with different crude oil sources, and compares the metabolic capability of soil bacteria with reference to different contamination sources and the age of the contaminated site. The results indicate that organic carbon and total nitrogen derived from petroleum hydrocarbon negatively affect microbial diversity. Contamination levels vary widely on site, with levels of PAHs ranging from 5.04 to 1.66 × 10³ μg kg^-1 and 6.20 to 5.64 × 10³ μg kg^-1 in Assam and Gujarat sites respectively, covering a higher proportion of low molecular weight (LMW) PAHs (fluorene, phenanthrene, pyrene, and anthracene). Functional diversity values were observed to be positively correlated (p < 0.05) with acenaphthylene, fluorene, anthracene, and phenanthrene. Microbial diversity was the highest in fresh oily sludge which decreased upon storage, indicating that immediate bioremediation, soon after its generation, would be beneficial. Improvement in the bio-accessibility of hydrocarbon compounds by the treatment of biosurfactant produced by a (soil isolate/isolate) was demonstrated., with respect to substrate utilization.

The Use of Raw Poultry Waste as Soil Amendment Under Field Conditions Caused a Loss of Bacterial Genetic Diversity Together with an Increment of Eutrophic Risk and Phytotoxic Effects

Poultry waste has been used as fertilizer to avoid soil degradation caused by the long-term application of chemical fertilizer. However, few studies have evaluated field conditions where livestock wastes have been used for extended periods of time. In this study, physicochemical parameters, metabarcoding of the 16S rRNA gene, and ecotoxicity indexes were used for the characterization of chicken manure and poultry litter to examine the effect of their application to agricultural soils for 10 years. Poultry wastes showed high concentrations of nutrients and increased electrical conductivity leading to phytotoxic effects on seeds. The bacterial communities were dominated by typical members of the gastrointestinal tract, noting the presence of pathogenic bacteria. Soils subjected to poultry manure applications showed statistically higher values of total and extractable phosphorous, increasing the risk of eutrophication. Moreover, while the soil bacterial community remained dominated by the ones related to the biogeochemical cycles of nutrients and plant growth promotion, losses of alpha diversity were observed on treated soils. Altogether, our work would contribute to understand the effects of common local agricultural practices and support the adoption of the waste treatment process in compliance with environmental sustainability guidelines.

Soil Microbial Network Complexity Varies With pH as a Continuum, Not a Threshold, Across the North China Plain

There has been little study on the biogeographical patterns of microbial co-occurrence, especially in agricultural soils. Here we investigated the biogeographical patterns and major drivers of co-occurrence network topological structure, and the relative abundance of keystone taxa for soil bacterial and fungal communities using high-throughput sequencing on a set of 90 samples across a 1,092 km transect in wheat fields of the North China Plain (NCP). We found that pH was the most important environmental factor driving network topology and relative abundance of keystone taxa. For the metacommunity composed of both bacteria and fungi, and for the bacterial community alone, lower soil pH was associated with a more complex microbial network. However, the network for fungi showed no strong trend with soil pH. In addition, keystone taxa abundance was positively correlated with ecosystem function and stability, and best explained by pH. Our results present new perspectives on impacts of pH on soil microbial network structure across large scales in agricultural environments. This improved knowledge of community processes provides a step toward understanding of functioning and stability of agricultural ecosystems.

Multikingdom interactions govern the microbiome in subterranean cultural heritage sites

SignificanceThe conservation of historical relics against microbial biodeterioration is critical to preserving cultural heritages. One major challenge is our limited understanding of microorganisms' dispersal, colonization, and persistence on relics after excavation and opening to external environments. Here, we investigate the ecological and physiological profiles of the microbiome within and outside the Dahuting Han Dynasty Tomb with a 1,800-y history. Actinobacteria dominate the microbiome in this tomb. Via interkingdom signaling mutualism, springtails carry Actinobacteria as one possible source into the tomb from surrounding environments. Subsequently, Actinobacteria produce cellulases combined with antimicrobial substances, which helps them to colonize and thrive in the tomb via intrakingdom competition. Our findings unravel the ecology of the microbiomes colonizing historical relics and provide help for conservation practices.

Corrigendum: Application of a Medical Diode Laser (810 nm) for Disinfecting Small Microbiologically Contaminated Spots on Degraded Collagenous Materials for Improved Biosafety in Objects of Exceptional Historical Value From the Auschwitz-Birkenau State Museum and Protection of Human Health

[This corrects the article DOI: 10.3389/fmicb.2020.596852.].

Application of a Medical Diode Laser (810 nm) for Disinfecting Small Microbiologically Contaminated Spots on Degraded Collagenous Materials for Improved Biosafety in Objects of Exceptional Historical Value From the Auschwitz-Birkenau State Museum and Protection of Human Health

The research aim was to optimize the operating parameters of a diode laser irradiation for the effective disinfection of degraded collagenous materials. Historical leather shoes stored at the Auschwitz-Birkenau State Museum in Oświęcim (Poland) were the main study objects. Surfaces of contaminated small spots occurring on the degraded materials were sampled with moistened swabs and microbiologically examined using the molecular techniques MALDI-TOF MS, 16S rRNA, and NGS sequencing. The surfaces were colonized by bacteria with 10⁶ CFU/100 cm² and 10⁴ CFU/100 cm² by fungi, on average. Microorganisms of the genera Bacillus and Penicillium were predominant. The effectiveness of the laser treatment was assessed for the new and degraded collagenous materials against isolated environmental strains using four variants of exposure time and number of repetitions. 0.3 W/CW 2 × 2 min variant was the most effective and also did not noticeably change the color of the treated samples. The variant caused a reduction in the numbers of microorganisms by 96–100%. After 1 month, four types of leather were subjected to comprehensive physico-chemical analyses. SEM and FTIR techniques confirmed that laser irradiation in the selected optimal variant did not affect the surface morphology and collagen structure, while XPS technique enabled detection of subtle changes in non-historical protective coatings on the surfaces of tested degraded historical materials.

Biological Risk for Hypogea: Shared Data from Etruscan Tombs in Italy and Ancient Tombs of the Baekje Dynasty in Republic of Korea

Biological growth represents one of the main threats for the conservation of subterranean cultural heritage. Knowledge of the conditions which favour the various taxonomic groups is important in delineating their control methods. Combining our experience regarding hypogea in Italy and the Republic of Korea, we aim to perform a critical review and comparison of the Biodeterioration Patterns (BPs) found, the materials used, and the conservative treatments applied. For this purpose, we focused on Etruscan tombs (Italy, 7th to 3th century BC) and the ancient tombs of the Baekje Dynasty (Republic of Korea, 6th to 7th centuries AD), most of which have been designated UNESCO World Heritage Sites, collecting original and bibliographic data as well as official documents. Results highlight the rich biodiversity of the bacterial and fungal species. Phototrophs were observed only in niches with sufficient light and the development of roots was also detected. Changes in humidity and temperature, the nature of the soil, nutrient accumulation, and vegetation above the hypogea along with human activities explain the different BPs. The effects of biocide treatments are also discussed, such as the emergence of dangerous fungal species. The shared data also enhance the role of overlaying tumuli and vegetation as well as protective barriers to reduce biological risk.

Antibiotic resistance gene profiling in response to antibiotic usage and environmental factors in the surface water and groundwater of Honghu Lake, China

There is an increasing concern that aquaculture has been implicated in the formation of antibiotic resistance gene (ARG) reservoirs; however, little is known about the consequences of their presence in groundwater. In this study, 22 antibiotics, including four acetylated metabolites, and 27 ARGs were analyzed in fish pond water, surface water, and groundwater of the Honghu Lake in China. Correlations between conventional parameters, ionic composition, antibiotic concentration, and relative abundance of ARGs in water samples were analyzed. Among the three different sources of water, total antibiotic levels were the highest in fish pond water and the lowest in groundwater, with moderate levels in lake water. In surface water, sulfonamides and their metabolites accounted for the highest antibiotic content, whereas tetracyclines were the most frequently found in groundwater samples. Despite the near-undetectable levels of antibiotics in groundwater, the relative abundance of ARGs in groundwater samples was even higher than that in surface waters. The magnitude and extent of ARG migration are likely to be dependent on local antibiotic contamination levels as well as on the local environmental and hydrogeological conditions, with the class 1 integrons (intI1) being essential for the dissemination of such ARGs. The effects of environmental parameters such as antibiotics, dissolved oxygen, HCO3-, and pH on ARGs were highly significant, reflecting the potential impact of these factors on the abundance of ARGs. Our findings thus highlight the need for improved control of the spread of ARGs in and from aquaculture environments.

Humidity governs the wall-inhabiting fungal community composition in a 1600-year tomb of Emperor Yang

Biodeterioration caused by filamentous fungi is often a threat to the architectural heritage (i.e. tombs and historic sites). To specifically understand the deterioration phenomena caused by microorganisms in tombs and how these are shaped due to various environmental factors, the fungal communities in the coffin chamber of the Chinese emperor Yang (BC 569-618) were investigated at different heights using denaturant gradient gel electrophoresis (DGGE) fingerprinting. The associated environmental conditions, such as humidity, temperature, height and illumination, were also assessed. The results showed that a great diversity of fungal species (Cordyceps, Fusarium, Harpochytrium, Emericellopsis, Volutella, Cladosporium, Stachybotrys, Trichoderma, Cochlonema and two unknown fungal species) was present in emperor Yang's coffin chamber. The predominant species were Stachybotrys, Fusarium, Trichoderma and Cochlonema. Redundancy analysis (RDA) indicated that humidity, temperature, height and illumination were the most significantly related factors shaping the fungal communities. Humidity showed the highest degree of variance description (19.2%) than all other environmental factors, followed by illumination (18.3%) and height (12.8%). Furthermore, fungal richness and diversity indices showed a positive correlation with humidity (p < 0.05). These results help in understanding the fungal community in tombs, promoting the mitigation of deterioration phenomena of such building heritage for the present and future.

Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing

Black garlic is a distinctive garlic deep-processed product made from fresh garlic at high temperature and controlled humidity. To explore microbial community structure, diversity and metabolic potential during the 12days of the black garlic processing, Illumina MiSeq sequencing technology was performed to sequence the 16S rRNA V3-V4 hypervariable region of bacteria. A total of 677,917 high quality reads were yielded with an average read length of 416bp. Operational taxonomic units (OTU) clustering analysis showed that the number of species OTUs ranged from 148 to 1974, with alpha diversity increasing remarkably, indicating the high microbial community abundance and diversity. Taxonomic analysis indicated that bacterial community was classified into 45 phyla and 1125 distinct genera, and the microbiome of black garlic samples based on phylogenetic analysis was dominated by distinct populations of four genera: Thermus, Corynebacterium, Streptococcus and Brevundimonas. The metabolic pathways were predicted for 16S rRNA marker gene sequences based on Kyoto Encyclopedia of Genes and Genomes (KEGG), indicating that amino acid metabolism, carbohydrate metabolism and membrane transport were important for the black garlic fermentation process. Overall, the study was the first to reveal microbial community structure and speculate the composition of functional genes in black garlic samples. The results contributed to further analysis of the interaction between microbial community and black garlic components at different stages, which was of great significance to study the formation mechanism and quality improvement of black garlic in the future.