Involvement of laccase-like enzymes in humic substance degradation by diverse polar soil bacteria

Humic substances modulate bacterial communities and mitigate adverse effects of temperature stress in coral reef organisms

AIMS

In the present study, we tested whether terrestrially derived humic substances (HS) could mitigate the adverse effects of elevated temperature and ultraviolet B (UVB) radiation on the bacterial communities of two hard corals (Montipora digitata and M. capricornis), one soft coral (Sarcophyton glaucum), sediment and water. We also examined the impact of temperature, UVB radiation, and HS supplementation on coral photosynthetic activity, a proxy for coral bleaching.

METHODS AND RESULTS

We performed a multifactorial experiment using a randomized-controlled microcosm setup. Coral photosynthetic efficiency was measured in vivo using a pulse amplitude modulation fluorometer. Bacterial communities were analyzed using 16S rRNA gene sequencing. Corals in HS-supplemented microcosms had significantly higher photosynthetic activities than those in microcosms subjected to elevated temperature and UVB radiation. Additionally, HS supplementation significantly influenced the composition of sediment, water, and host-associated bacterial communities. Reef organisms in HS supplemented microcosms contained distinct bacterial communities enriched with groups of potentially beneficial bacteria. In the hard coral M. digitata, we observed an interactive effect of HS supplementation, UVB radiation, and temperature.

CONCLUSION

Our findings indicate that HS significantly modulates coral reef bacterial communities and support the hypothesis that these substances contribute to improved reef resistance to the adverse effects of elevated temperature and UVB radiation.

Thermophilic bacteria contributing to humus accumulation in hyperthermophilic aerobic fermentation of mushroom residue

The purpose of this study is to clarify the roles of thermophilic bacteria in humification during hyperthermophilic composting (HTC) of organic wastes mainly composed of mushroom residue. Results showed that HTC with a long hyperthermophilic (>80°C) period lasting for 18 days produced 83 mg/g of humus in compost on day 27, significantly higher than that of thermophilic composting (TC, 9.7 mg/g). Machine learning models identified that the dominant thermophiles belonging to Bacillaceae, Sporolactobacillaceae, Thermaerobacteraceae, Paenibacillaceae families and the unique thermophiles (Thermus and Calditerricola) in HTC played important roles in accumulating stubborn and soluble humus including humic acid and fulvic acid. Hyperthermophilic fermentation not only recruited and enriched these thermophilic bacteria to rapidly degrade organic matter into bioavailable nutrients, but also upregulated the metabolic pathways relevant to the generation and oxidation of precursors including amino acids that would be polymerized into humus, thus efficiently converting organic waste into humus-rich compost.

Facilitating effects of plant extracts on soil health and replanted Panax ginseng growth in recession soil

BACKGROUND

Plant extracts have been shown to be effective agricultural strategies for improving soil fertility and quality, and promoting plant growth in soil degradation remediation. The application of plant extracts improves the material cycle of soil microecology, such as the decomposition of nitrogen, phosphorus, and potassium, while increasing plant resistance. However, there is currently no experiment to demonstrate whether plant extracts have a promoting effect on the growth of ginseng and the mechanism of action.

OBJECTIVES AND METHODS

Pot experiments were carried out to investigate the effects of extracts, namely Rubia cordifolia (RC), Schisandra chinensis (SC), and Euphorbia humifusa (EH) on soil properties, enzyme activities, and plant physiological characteristics were evaluated.

RESULTS

Results showed that compared with CK, plant extract-related treatments increased soil Organic carbon (OC), Available nitrogen (AN), Available phosphorus (AP) contents, and Soil urease activity. (S-UE), Soil sucrase activity (Soil sucrase), Soil acid phosphatase activity. (S-ACP). Meanwhile, plant extract-related treatments significantly increased plant physiological properties and TP (Total protein) content, and decreased the content of MDA (malondialdehyde) by 15.70% -36.59% and PRO (proline) by 30.13% -148.44%. Furthermore, plant extract-related treatments also significantly promote plant growth and reduce plant incidence, the fresh weight of ginseng increased by 27.80% -52.08%, ginseng root activity increased by 45.13% -90.07%, and ginseng incidence rate decreased by 20.00% -46.67%. Through correlation analysis between fresh weight of ginseng and root parameters and soil index, fresh weight is significantly positively correlated with root diameter, fiber root number, root activity, total protein (TP), catalytic activity (CAT) and superoxide dismutase activity (SOD), H, soil urea activity (S-UE), soil sucrose activity (S-SC), soil acid phosphate activity (S-ACP), and soil laccase activity (SL); The fresh weight was significantly negatively correlated with incidence rate, disease severity index, and malondialdehyde content (MDA).

CONCLUSION

In summary, plant extract-related treatments improve soil quality and promote ginseng growth, further enhancing soil health and plant disease resistance. These findings provide new insights into ginseng cultivation and soil health management and highlight a new approach that can be applied to a wider range of agricultural practices and environmental sustainability.

Kraft Lignin Decomposition by Forest Soil Bacterium Pseudomonas kribbensis CHA-19

Identification of the biochemical metabolic pathway for lignin decomposition and the responsible degradative enzymes is needed for the effective biotechnological valorization of lignin to renewable chemical products. In this study, we investigated the decomposition of kraft lignin by the soil bacterium Pseudomonas kribbensis CHA-19, a strain that can utilize kraft lignin and its main degradation metabolite, vanillic acid, as growth substrates. Gel permeation chromatography revealed that CHA-19 decomposed polymeric lignin and degraded dehydrodivanillin (a representative lignin model compound); however, the degradative enzyme(s) and mechanism were not identified. Quantitative polymerase chain reaction with mRNAs from CHA-19 cells induced in the presence of lignin showed that the putative genes coding for two laccase-like multicopper oxidases (LMCOs) and three dye-decolorizing peroxidases (DyPs) were upregulated by 2.0- to 7.9-fold compared with glucose-induced cells, which indicates possible cooperation with multiple enzymes for lignin decomposition. Computational homology analysis of the protein sequences of LMCOs and DyPs also predicted their roles in lignin decomposition. Based on the above data, CHA-19 appears to initiate oxidative lignin decomposition using multifunctional LMCOs and DyPs, producing smaller metabolites such as vanillic acid, which is further degraded via ortho- and meta-ring cleavage pathways. This study not only helps to better understand the role of bacteria in lignin decomposition and thus in terrestrial ecosystems, but also expands the biocatalytic toolbox with new bacterial cells and their degradative enzymes for lignin valorization.

Bioprospecting the potential of the microbial community associated to Antarctic marine sediments for hydrocarbon bioremediation

Microorganisms that inhabit the cold Antarctic environment can produce ligninolytic enzymes potentially useful in bioremediation. Our study focused on characterizing Antarctic bacteria and fungi from marine sediment samples of King George and Deception Islands, maritime Antarctica, potentially affected by hydrocarbon influence, able to produce enzymes for use in bioremediation processes in environments impacted with petroleum derivatives. A total of 168 microorganism isolates were obtained: 56 from sediments of King George Island and 112 from Deception Island. Among them, five bacterial isolates were tolerant to cell growth in the presence of diesel oil and gasoline and seven fungal were able to discolor RBBR dye. In addition, 16 isolates (15 bacterial and one fungal) displayed enzymatic emulsifying activities. Two isolates were characterized taxonomically by showing better biotechnological results. Psychrobacter sp. BAD17 and Cladosporium sp. FAR18 showed pyrene tolerance (cell growth of 0.03 g mL-1 and 0.2 g mL-1) and laccase enzymatic activity (0.006 UL-1 and 0.10 UL-1), respectively. Our results indicate that bacteria and fungi living in sediments under potential effect of hydrocarbon pollution may represent a promising alternative to bioremediate cold environments contaminated with polluting compounds derived from petroleum such as polycyclic aromatic hydrocarbons and dyes.

Potential of Medicago sativa and Perilla frutescens for overcoming the soil sickness caused by ginseng cultivation

There are serious soil sickness in ginseng cultivation. Crop rotation is an effective agricultural management to improve soil sustainability and reduce soil sickness. To explore an appropriate ginseng rotation system, Medicago sativa (alfalfa) and Perilla frutescens (perilla) were planted on ginseng cultivation soil for 1 year to evaluate the improvement effect of both. Through chemical analysis and high-throughput sequencing technology, we found that after alfalfa and perilla cultivation for one-year, various nutrients and enzyme activities in ginseng cultivation soil were significantly improved. In addition, perilla significantly increased the diversity and richness of soil fungal communities. Cultivation of alfalfa and perilla significantly changed the composition of soil bacterial and fungal communities and significantly reduced the abundance of the potentially pathogenic fungi Ilyonectria. Further pot experiments also showed that the improved soil could significantly increase root activity of ginseng plant after two plants were planted. It should be noted that, unlike alfalfa, perilla decreased soil electrical conductivity, increased soil organic matter, soil urease, and may significantly improve the diversity and richness of soil fungal community. Moreover, in the pot experiment, the root fresh weight of ginseng cultured in perilla treated soil increased significantly. This study highlights that perilla may have better soil improvement effect than alfalfa and it has the potential to be used in the soil improvement of ginseng cultivation.

Chemical structure and nanomechanics relevant electrochemistry of solid-phase humic acid along a typical forest-river-paddy landscape section in eastern China and its environmental implications

Solid-phase humic acid (HA_solid) plays a critical role in global carbon cycle and redox biogeochemistry of topsoil, because of its unique physicochemical properties, including electrochemical property. In this study, topsoil HA_solid along a typical forest-river-paddy landscape section in eastern China was investigated in the aspects of electrochemical property, chemical structure and nanomechanics, and their relationship. Nano-size HA_solid particles were extracted from topsoil of paddy soil (PS-HA_solid), forest soil (FS-HA_solid) and riverside sediment (RS-HA_solid). Results showed that all the HA_solid were conductive and played an important role in conductivity of topsoil suspension. HA_solid contained both reversible and irreversible redox peaks, with redox activity of PS-HA_solid > RS-HA_solid > FS-HA_solid. Owing to limited humification, electron exchange capacity (EEC) values of topsoil HA_solid suspensions were modest (3.18-4.45 μmol e^-g^-1 HA_solid). Compared with RS-HA_solid and FS-HA_solid, PS-HA_solid showed higher aromaticity and higher degree of humification with simple and even nanomechanical property. Long-term cultivation (human activities) as well as high content of polyvalent metals in paddy soil were supposed to facilitate formation of aromatic carbon and improve humification of HA_solid. The results suggested that aromatic carbon and high humification degree of PS-HA_solid contributed to simple and even nanomechanics, which further optimized its electrochemical property. This study not only provides novel insight into the mechanism of HA_solid mediating electron transfer, but also inspires ideas for soil and environmental management with different purposes based on regulation of HA_solid.

Different Responses of Soil Environmental Factors, Soil Bacterial Community, and Root Performance to Reductive Soil Disinfestation and Soil Fumigant Chloropicrin

Reductive soil disinfestation (RSD) and soil fumigant chloropicrin (SFC) are two common agricultural strategies for the elimination of soil-borne pathogens. However, the differences in soil environmental factors, soil bacterial microbiome, and root performance between SFC and RSD are poorly understood. In this study, three soil treatments, untreated control (CK), SFC with 0.5 t⋅ha–1 chloropicrin, and RSD with 15 t⋅ha–1 animal feces, were compared. We evaluated their effects on soil environmental factors, bacterial community structure, and root activity using chemical analysis and high-throughput sequencing. RSD treatment improved soil composition structure, bacterial diversity, and root performance to a greater extent. Carbon source utilization preference and bacterial community structure were strikingly altered by SFC and RSD practices. Bacterial richness, diversity, and evenness were notably lowered in the SFC- and RSD-treated soil compared with the CK-treated soil. However, RSD-treated soil harbored distinct unique and core microbiomes that were composed of more abundant and diverse potentially disease-suppressive and organic-decomposable agents. Also, soil bacterial diversity and composition were closely related to soil physicochemical properties and enzyme activity, of which pH, available Na (ANa), available Mg (AMg), available Mn (AMn), total Na (TNa), total Ca (TCa), total Cu (TCu), total Sr (TSr), urease (S-UE), acid phosphatase (S-ACP), and sucrase (S-SC) were the main drivers. Moreover, RSD treatment also significantly increased ginseng root activity. Collectively, these results suggest that RSD practices could considerably restore soil nutrient structure and bacterial diversity and improve root performance, which can be applied as a potential agricultural practice for the development of disease-suppressive soil.

Temperature sensitivity of Antarctic soil-humic substance degradation by cold-adapted bacteria

Heteropolymer humic substances (HS) are the largest constituents of soil organic matter and are key components that affect plant and microbial growth in maritime Antarctic tundra. We investigated HS decomposition in Antarctic tundra soils from distinct sites by incubating samples at 5°C or 8°C (within a natural soil thawing temperature range of -3.8°C to 9.6°C) for 90 days (average Antarctic summer period). This continuous 3-month artificial incubation maintained a higher total soil temperature than that in natural conditions. The long-term warming effects rapidly decreased HS content during the initial incubation, with no significant difference between 5°C and 8°C. In the presence of Antarctic tundra soil heterogeneity, the relative abundance of Proteobacteria (one of the major bacterial phyla in cold soil environments) increased during HS decomposition, which was more significant at 8°C than at 5°C. Contrasting this, the relative abundance of Actinobacteria (another major group) did not exhibit any significant variation. This microcosm study indicates that higher temperatures or prolonged thawing periods affect the relative abundance of cold-adapted bacterial communities, thereby promoting the rate of microbial HS decomposition. The resulting increase in HS-derived small metabolites will possibly accelerate warming-induced changes in the Antarctic tundra ecosystem.