Zhongjun Jia

• Ph.D
• Head of Department at Chinese Academy of Sciences

【Objective】Potassium-solubilizing bacteria (KSB) are considered key plant growth-promoting bacteria for the sustainable development of ecological agriculture due to their unique advantage of potassium solubilization. To fully explore the resources of potassium-solubilizing bacteria in the environment, the changes in the characteristics of soil pota...

Purpose Soil microbiome plays a crucial role in maintaining soil fertility and nutrient cycling, offering potential solutions for soil restoration. However, there remains a notable gap in the understanding of how bacterial communities respond to soil dealkalinization. The research aims to investigate the microbial dynamics of soil bacterial communi...

Actinomycetota are unrivalled producers of bioactive natural products, with strains living in association with macroalgae representing a prolific—yet largely unexplored—source of specialised chemicals. In this work, we have investigated the bioactive potential of Actinomycetota from macroalgae through culture‐dependent and ‐independent approaches....

Microbial methane oxidation under widespread suboxic environment is crucial for understanding methane emission. However, the role of aerobic methanotrophs in mediating methane oxidation and nitrogen fixation is less understood in oxygen-limiting environments. In this study, we identified diazotrophic methanotrophs under oxygen-limited conditions (i...

Abstract: By using conventional bacteria medium (BPM), inorganic phosphate-solubilizing bacteria (PSB) medium (IPM) and organic PSB medium (OPM), culturable microbial colonies were collected after third serial passage on agar plates. High-throughput sequencing analysis of phoD gene as molecular target were employed to evaluate the diversity differe...

Soil microorganisms play a crucial role in suppressing soil-borne diseases. Although the composition of microbial communities in healthy versus diseased soils is somewhat understood, the interplay between microbial interactions and disease incidence remains unclear. This study used 16S rRNA and fungal internal transcribed spacer (ITS) sequencing to...

【Objective】High-throughput sequencing technology was used to study the changes in the diversity of culturable phosphate-solubilizing bacteria (PSB) during serial enrichment, to evaluate the effects of different media and generations on diversity assessment of culturable PSB in paddy soil.【Methods】Through serial passages with inorganic phosphorus me...

Land use changes soil microbial and chemical properties, but the mechanism of biological nitrogen fixation under different land use patterns is rarely reported, so we used four types of soil: Natural forest soil (NS), healthy banana soil (HS), diseased banana soil (DS) and paddy soil (PS). Treatments included the control (CK), addition of glucose (...

The root-associated type II methanotrophs significantly contribute to CH4 oxidation-dependent N2 fixation. However, it is unclear whether type I methanotrophs are involved in CH4 oxidation and N2 fixation, especially in natural wetlands. So far, limited attention has given to root-associated active microorganisms. Here, metatranscriptomic analysis...

Actinomycetota, associated with macroalgae, remains one of the least explored marine niches. The secondary metabolism of Actinomycetota, the primary microbial source of compounds relevant to biotechnology, continues to drive research into the distribution, dynamics, and metabolome of these microorganisms. In this study, we employed a combination of...

Soil microorganisms play an important role in soil ecosystems as the main decomposers of carbon and nitrogen. They have an indispensable impact on soil health, and any alterations in the levels of organic carbon and inorganic nitrogen can significantly affect soil chemical properties and microbial community composition. Previous studies have focuse...

The presence and spread of antimicrobial resistance genes (ARGs) in soil represent a significant threat to human health. However, the ARGs harbored by antibiotic-degrading microorganisms in soil are inadequately characterized. Employing diverse molecular techniques, we investigate the dynamics of ARGs, mobile genetic elements, and virulence factors...

Agricultural waterways are often contaminated with herbicide and antibiotic residues due to the widespread use of these chemicals in modern agriculture. The search for resistant bacterial strains that can adapt to and degrade these mixed contaminants is essential for effective in situ bioremediation. Herein, by integrating chemical and transcriptom...

Abstract:【Objective】Nitrifiers play an important role in the process of farmland soil nitrogen transformation. A study on the distribution of nitrifying microorganisms in aggregates will help to reveal the interaction mechanism between soil structure, microorganisms and soil nutrient cycling.【Method】The changes in soil aggregate properties and nitr...

The primary purpose of our study is to clarify the differences in physicochemical properties and microbial community composition with the continuous evolution of soil utilization types. Here, we used natural forest soil (NS), healthy banana garden soil (HS), diseased banana garden soil (DS), and paddy soil (PS) in tropical areas of Hainan Province...

Non-alcoholic steatohepatitis (NASH) is the severe form of non-alcoholic fatty liver disease, and is characterized by liver inflammation and fat accumulation. Dietary interventions, such as fibre, have been shown to alleviate this metabolic disorder in mice via the gut microbiota. Here, we investigated the mechanistic role of the gut microbiota in...

Background Methane (CH4) oxidation driven by soil aerobic methanotrophs demonstrates the capacity of grassland as a CH4 sink. Methods In this study, we compared the oxidation characteristics of atmospheric‐level and elevated concentration (10%) CH4 in a typical grassland (steppe) on the Loess Plateau, an alpine meadow (meadow) on the Qinghai‐Tibet...

Crop rotation can assemble distinct core microbiota as functionally specific barriers against the invasion of banana Fusarium oxysporum pathogens. However, the taxonomic identity of rotation‐unique core taxa and their legacy effects are poorly understood under field conditions. Pepper and eggplant rotations were employed to reveal rotation crop‐ an...

Ammonia oxidation is the rate-limiting step of the global nitrogen cycle, and it is mainly catalyzed by ammonia-oxidizing bacteria (AOB) and archaea (AOA). AOA can carry out nitrification even in acidic soils, whereas AOB activity was not consistently observed in acidic soils. In this study, we manipulated two environmental variables, i.e., the mic...

Bathyarchaeota is believed to play a crucial role in the global carbon cycle due to its vast biomass, broad distribution, and diverse habitat. However, its physiological and metabolic features are hard to determine without pure culture. While metagenomic analyses have shown that Bathyarchaeota has a complete inorganic carbon fixation (Wood-Ljungdah...

Simple Summary The effects of increasing temperature and dietary lipid level on the body composition, growth performance, and freshness profile of the European seabass (Dicentrarchus labrax) were evaluated through a fish trial lasting 56 days. Findings demonstrated that fish reared at 24 °C presented a lower lipid level and a higher daily growth in...

Plant uptake of nitrogen is often associated with increased incidence of banana Fusarium wilt, a disease caused by the soil-borne fungus Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). However, the nitrogen metabolic preferences of Foc TR4 pathogens remain unknown. In this study, we investigated the ecophysiological patterns of Foc TR4...

This Supplementary file includes: Supplementary Materials and Methods Supplementary Results and Discussion Supplementary References Supplementary Figs. S1 to S4 Supplementary Tables S1 to S6

Correction to: ISME Communications https://doi.org/10.1038/ s43705-021-00068-2, published online 9 December 2021 The “CH4 emissions” should be “CH4 uptake” in the sentence of “Grazing significantly decreases CH4 emissions while it increases N2O emissions basing on 14-month in situ measurement” The correct sentence should be read: Grazing significan...

The extensive use of organic chemicals has resulted in the widespread distribution of hydrocarbon contaminants (HCs) in many ecosystems on a global scale. Many subterranean ecosystems can rapidly become anaerobic or even methanogenic following hydrocarbon contamination. Bacteria and archaea dominate communities in such systems and mediate the syntr...

Members of genus Nitrospira represent the most diverse nitrite-oxidizing bacteria (NOB) and are ubiquitous in terrestrial ecosystems, which complete the nitrification process by converting nitrite to nitrate. NOB has shown physiological adaptation to a wide range of environmental conditions, including extreme pH and salinity. However, little is kno...

Banana Fusarium wilt-suppressive soils are effective against pathogen invasion, yet soil physicochemical factors responsible for conducive or suppressive behavior have not been reported. Here, we investigated the changes in banana biomass, disease incidence (DI), soil culturable microbes and physicochemical properties by incorporating pepper and ba...

Soil microbiomes drive the biogeochemical cycling of nitrogen and regulate soil N supply and loss, thus, pivotal nitrogen use efficiency (NUE). Meanwhile, Front. Agr. Sci. Eng. https://doi.org/10.15302/J-FASE-2022450 REVIEW there is an increasing awareness that plant associated microbiomes and soil food web interactions is vital for modulating crop...

Soil methanotrophs are the only biological sink for atmospheric methane (CH4). The activity and the diversity of methanotrophic communities in grassland soils can be impacted by animal grazing. In this study, soils were collected from a 17-year running grazing intensity trial in a typical steppe in the Loess Plateau, China to examine the responses...

Soil heterotrophic respiration during decomposition of carbon (C)-rich organic matter plays a vital role in sustaining soil fertility. However, it remains poorly understood whether dinitrogen (N2) fixation occurs in support of soil heterotrophic respiration. In this study, ¹⁵N2-tracing indicated that strong N2 fixation occurred during heterotrophic...

Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitro...

The bioavailability of nitrogen constrains primary productivity, and ecosystem stoichiometry implies stimulation of N2 fixation in association with carbon sequestration in hotspots such as paddy soils. In this study, we show that N2 fixation was triggered by methane oxidation and the methanotrophs serve as microbial engines driving the turnover of...

The discovery of a complete ammonia oxidizer (comammox Nitrospira) challenged the traditional theory of two step nitrification. Comammox Nitrospira co-occurred and competed with traditional ammonia oxidizers in many habitats. However, the ubiquitous existence and high abundance of comammox Nitrospira in drinking-water treatment plants (DWTPs) sugge...

Human activities severely affect the global nitrogen (N) cycle. Croplands receive intensive N fertilization; consequently, cropland and natural ecosystem differentiation often results in community and functional variation in N-transforming microbes, including nitrifiers, which perform nitrification central to N cycle. However, evidence of such vari...

Biological methane oxidation is a crucial process in the global carbon cycle that reduces methane emissions from paddy fields and natural wetlands into the atmosphere. However, soil organic carbon accumulation associated with microbial methane oxidation is poorly understood. Therefore, to investigate methane-derived carbon incorporation into soil o...

Root-associated aerobic methanotroph plays an important role in reducing methane emissions from wetlands. In this study, we examined the activity of methane-dependent nitrogen fixation and active nitrogen-fixing bacterial communities on the roots of Typha angustifolia and Scirpus triqueter using a 15N-N2 feeding experiment and a cDNA-based clone li...

Denitrifying anaerobic methane oxidation (DAMO) microorganisms, using nitrate/nitrite to oxidize methane, have been proved to be an important microbial methane sink in natural habitats. Increasing nitrogen deposit around the globe brings increased availability of substrates for these microorganisms. However, how elevated nitrogen level affects deni...

Soil moisture is the major factor influencing microbial properties and nitrous oxide (N2O) production. Agricultural soils can be probed under wetting, wet/dry alternating, and constant moisture conditions to evaluate the combined effects of early (previous) and immediate (current) moisture on N2O emission and nitrification/denitrification. In view...

In this study, bioleaching was carried out for the recovery of metals (copper, zinc, tin, lead, gold and silver) from printed circuit boards residues (PCBs), one of the most important wastes from electrical and electronic equipment, using an acidophilic iron-oxidizing bacterial consortium enriched with minerals from a gold mine in the Arequipa regi...

Ammonia oxidising archaea (AOA) are ecologically important nitrifiers in acidic agricultural soils. Two AOA phylogenetic clades, belonging to order-level lineages of Nitrososphaerales (clade C11; also classified as NS-Gamma-2.3.2) and family-level lineage of Candidatus Nitrosotaleaceae (clade C14; NT-Alpha-1.1.1), usually dominate AOA population in...

This paper presents data on the net greenhouse gas balance (measured as CO2 equivalents) of N2O emitted and C fixed in nitrifying pastoral soils over a 10-week laboratory incubation period. In a low nitrogen environment without urine deposition, typical of large areas of grassland, archaeal-dominated nitrification increased soil organic carbon (SOC...

Grassland soils serve as a biological sink and source of the potent greenhouse gases (GHG) methane (CH4) and nitrous oxide (N2O). The underlying mechanisms responsible for those GHG emissions, specifically, the relationships between methane- and ammonia-oxidizing microorganisms in grazed grassland soils are still poorly understood. Here, we charact...

The intensified input of anthropogenic nitrogen (N) fertilizers has accelerated the transformation of active N species (e.g., N2O, NO3⁻ and NO2⁻) and the coupled methane (CH4) cycling on a global scale, but the impact of N-mediated CH4 metabolism on soil carbon accumulation, which is crucial for agricultural sustainability, remains poorly understoo...

Salt tolerance-based niche differentiation of soil ammonia oxidizers (The ISME Journal; https://doi.org/10.1038/s41396-021-01079-6)

Ammonia oxidizers are key players in the global nitrogen cycle, yet little is known about their ecological performances and adaptation strategies for growth in saline terrestrial ecosystems. This study combined 13C-DNA stable-isotope probing (SIP) microcosms with amplicon and shotgun sequencing to reveal the composition and genomic adaptations of a...

The Zoige wetland of the Tibetan Plateau is one of the largest alpine wetlands in the world and a major emission source of methane. Methane oxidation by methanotrophs can counteract the global warming effect of methane released in the wetlands. Understanding methanotroph activity, diversity, and metabolism at the molecular level can guide the isola...

Methane (CH4) emissions from Arctic lakes are a large and growing source of greenhouse gas to the atmosphere with critical implications for global climate. Because Arctic lakes are ice covered for much of the year, understanding the metabolic flexibility of methanotrophs under anoxic conditions would aid in characterizing the mechanisms responsible...

The emission pattern of greenhouse gas (GHG) has been intensively investigated in different agro-ecosystems, but the underlying microbial mechanism in soil is still poorly understood, especially under many possible measures for improving nitrogen utilization. Thus, a 28-day laboratory microcosm experiment was conducted with an upland soil to invest...

The accumulation of estrogens in aquatic environments has drawn increasing public concern due to their adverse effects on aquatic ecosystems and human health. Bacteria play important roles in eliminating estrogens from the environment, but knowledge of the identity and functions of the microorganisms involved in metabolizing these steroid hormones...

Little information is available about the effects of drought on soil methane (CH4) uptake and the underlying feedback of the soil microbial community in forest biomes. More importantly, a meta-analysis of the current literature on this topic revealed that there are virtually no data available in subtropical forests. To fill the abovementioned knowl...

Soil is home to an enormous and complex microbiome that features arguably the highest genomic diversity and metabolic heterogeneity of cells on Earth. Their in situ

Elevated atmospheric CO2 (eCO2) results in plant growth and N limitation, yet how root-associated nitrogen-fixing bacterial communities respond to increasing atmospheric CO2 and nitrogen fertilization (eN) during the growth stages of rice is unclear. Using the nifH gene as a molecular marker, we studied the combined effect of eCO2 and eN on the dia...

This study evaluated the use of Gracilaria by-products in gilthead seabream diet to modulate intestinal bacterial community, physiological responses as well as skin and fillet attributes during cold storage. Fish were fed for 52 days with six experimental diets: i) a diet containing a commercial antioxidant (CTR), ii) a diet without antioxidant (NO...

Microorganisms interact in complex communities, affecting microbially-mediated processes in the environment. Particularly, aerobic methanotrophs showed significantly stimulated growth and activity in the presence of accompanying microorganisms in an interaction network (interactome). Yet, little is known of how the interactome responds to disturban...

The response pattern of soil bacterial communities to drought events has been characterized from short-term laboratory desiccation and in naturally arid soils, but the resistance of soil bacteria to persistently long periods of desiccation remains largely unknown. This study assessed the abundance and composition of bacteria in 24 historical soils...

Chemoautotrophic canonical ammonia-oxidizers and complete ammonia oxidizers (comammox) are responsible for ammonia oxidation, which is the rate-limiting step of nitrification in terrestrial ecosystems. However, the relative importance of autotrophic nitrification and the related active nitrifiers during mineralization of organic substances with dif...

The discovery of complete ammonia oxidizer (comammox) was a breakthrough in the study of nitrification. However, slow growth of comammox bacteria makes it challenging to distinguish them from traditional ammonia oxidizing microorganisms. Genomic data indicated that comammox bacteria encoded genes that can metabolize urea and had higher nitrite tole...

Anaerobic oxidation of methane (AOM) coupled with simultaneous consumption of nitrous oxide (N2O) has been recently reported, but the underlying coupling mechanism remains unclear. Here, we investigated N2O-mediated AOM in paddy soil under amendment of electron shuttles (anthraquinone-2,6-disulphonate and methylviologen). Sixty-day anaerobic incuba...

Using DNA-based stable isotope probing (SIP) in microcosms, we demonstrate the shifts in active nitrifying communities in soil from field plots imposed by 8 years of mineral fertilizer N (NPK) or manure (M) applications compared with an unfertilized control (CK), and associated shifts in their temperature sensitivity. DNA-SIP indicates that ammonia...

Soil microbes play a key role in terrestrial ecosystems. In the saline-sodic environment, the microbial communities and their community assembly processes, especially throughout soil profiles, however, are not well understood. Here, we characterized the soil microbial communities across three sodicity/salinity gradients to 1.0 m depth in the wester...

Anaerobic oxidation of methane (AOM) plays an important role in regulating methane (CH4) emissions from coastal wetland ecosystems. In recent decades, coastal estuarine wetlands have been subjected to great environmental pressure associated with terrestrial nitrogen (N) input. Here, we used ¹³CH4 to quantify AOM rates in coastal wetland sediments w...

DNA-based stable isotope probing (DNA-SIP) was employed to establish direct link between methane oxidation activity and the taxonomic identity of active methanotrophs in three rice field soils from Jian-San-Jiang (one baijiang origin soil, JB and one meadow origin soil, JM) and Qing-An (meadow origin soil, QA) districts in Northeastern China. Follo...

Cadmium (Cd), chromium (Cr) and lead (Pb) are heavy metals that have been classified as priority pollutants in aqueous environment while methane-oxidizing bacteria as a biofilter arguably consume up to 90% of the produced methane in the same aqueous environment before it escapes into the atmosphere. However, the underlying kinetics and active metha...

Soil-borne Fusarium wilt disease causes damage to certain crops, but crop rotation may be an effective management strategy for this pest. Soil microbes may play an important role in this strategy, but the response of the soil microbial community to crop rotation is unclear. In a field experiment, we used high-throughput sequencing to study the effe...

The abundance and diversity of bacteria in 24 historical soil samples under air-dried storage conditions for more than 70 years were assessed by quantification and high-throughput sequencing analysis of 16S rRNA genes. All soils contained a measurable abundance of bacteria varying from 10 ³ to 10 ⁸ per gram of soil and contrasting community composi...

Methanotrophs are the only biofilters for reducing the flux of global methane (CH4) emissions in water-logged wetlands. However, adaptation of aerobic methanotrophs to low concentrations of oxygen and nitrogen in typical swamps, such as that of the Qinghai–Tibetan Plateau, is poorly understood. In this study, we show that Methylobacter-like methano...

The role of manipulated microcosms in microbial ecology has been much debated, because they cannot entirely represent the in situ situation. We collected soil samples from 20 field plots, including 5 different treatments with and without nitrogen fertilizers for 22 years, in order to assess active nitrifying communities by in situ transcriptomics a...

Upland soil clusters alpha and gamma (USCα and USCγ) are considered a major biological sink of atmospheric methane and are often detected in forest and grassland soils. These clusters are phylogenetically classified using the particulate methane monooxygenase gene pmoA because of the difficulty of cultivation. Recent studies have established a dire...

Solonetz soils are typically characterized with excessive saline-alkali content, and physiochemical methods are often employed for solonetz reclamation. However, increasing lines of evidences have suggested that micro-biomes play a pivotal role in sustaining soil fertility than previously appreciated, and it remains poorly understood about the taxo...

Microorganisms may reciprocally select for specific interacting partners, forming a network with interdependent relationships. The methanotrophic interaction network, comprising of methanotrophs and non-methanotrophs, is thought to modulate methane oxidation and give rise to emergent properties beneficial for the methanotrophs. Therefore, microbial...