Wenhui Zhong

The effects of mineral fertilizer and organic manure on soil microbial community and diversity

The effects of mineral fertilizer (NPK) and organic manure on phospholipid fatty acid profiles and microbial functional diversity were investigated in a long-term (21-year) fertilizer experiment. The experiment included nine treatments: organic manure (OM), organic manure plus fertilizer NPK (OM + NPK), fertilizer NPK (NPK), fertilizer NP (NP), fertilizer NK (NK), fertilizer N (N), fertilizer P (P), fertilizer K (K), and the control (CK, without fertilization). The original soil was extremely eroded, characterized by low pH and deficiencies of nutrients, particularly N and P. The application of OM and OM + NPK greatly increased crop yields, soil pH, organic C, total N, P and K, available N, P and K content. Crop yields, soil pH, organic C, total N and available N were also clearly increased by the application of mineral NPK fertilizer. The amounts of total PLFAs, bacterial, Gram-negative and actinobacterial PLFAs were highest in the OM + NPK treatment, followed by the OM treatment, whilst least in the N treatment. The amounts of Gram-positive and anaerobic PLFAs were highest in the OM treatment whilst least in the P treatment and the control, respectively. The amounts of aerobic and fungal PLFAs were highest in the NPK treatment whilst least in the N and P treatment, respectively. The average well color development (AWCD) was significantly increased by the application of OM and OM + NPK, and the functional diversity indices including Shannon index (H′), Simpson index (D) and McIntosh index (U) were also significantly increased by the application of OM and OM + NPK. Principal component analysis (PCA) of PLFA profiles and C source utilization patterns were used to describe changes in microbial biomass and metabolic fingerprints from nine fertilizer treatments. The PLFA profiles from OM, OM + NPK, NP and NPK were significantly different from that of CK, N, P, K and NK, and C source utilization patterns from OM and OM + NPK were clearly different from organic manure deficient treatments (CK, N, P, K, NP, NK 6 and NPK). Stepwise multiple regression analysis showed that total N, available P and soil pH significantly affected PLFA profiles and microbial functional diversity. Our results could provide a better understanding of the importance of organic manure plus balanced fertilization with N, P and K in promoting the soil microbial biomass, activity and diversity and thus enhancing crop growth and production.

Transgenic Bt rice has adverse impacts on CH4 flux and rhizospheric methanogenic archaeal and methanotrophic bacterial communities

Background and AimsThe effect of transgenic insect-resistant crops on soil microorganisms has become an issue of public concern. The goal of this study was to firstly realize the variation of in situ methane (CH4) emission flux and methanogenic and methanotrophic communities due to planting transgenic Bt rice (Bt) cultivar.MethodsCH4 emitted from paddy soil was collected by static closed chamber technique. Denaturing gradient gel electrophoresis and real-time PCR methods were employed to analyze methanogenic archaeal and methanotrophic bacterial community structure and abundance.ResultsResults showed that planting Bt rice cultivar effectively reduced in situ CH4 emission flux and methanogenic archaeal and methanotrophic bacterial community abundance and diversity. Data analysis showed that in situ CH4 emission flux increased significantly with the increase of methanogenic archaeal abundance (R2 = 0.839, p < 0.001) and diversity index H′ (R2 = 0.729, p < 0.05), whereas was not obviously related to methanotrophic bacterial community.ConclusionsOur results suggested that the lower in situ CH4 emission flux from Bt soil may result from lower methanogenic archaeal community abundance and diversity, lower methanogenic activity and higher methanotrophic activity. Moreover, our results inferred that specific functional microorganisms may be a more sensitive indicator than the total archaeal, bacterial or fungal population to assess the effects of transgenic insect-resistant plants on soil microorganisms.

Characterization of Electricity Generated by Soil in Microbial Fuel Cells and the Isolation of Soil Source Exoelectrogenic Bacteria

Soil has been used to generate electrical power in microbial fuel cells (MFCs) and exhibited several potential applications. This study aimed to reveal the effect of soil properties on the generated electricity and the diversity of soil source exoelectrogenic bacteria. Seven soil samples were collected across China and packed into air-cathode MFCs to generate electricity over a 270 days period. The Fe(III)-reducing bacteria in soil were enriched and sequenced by Illumina pyrosequencing. Culturable strains of Fe(III)-reducing bacteria were isolated and identified phylogenetically. Their exoelectrogenic ability was evaluated by polarization measurement. The results showed that soils with higher organic carbon (OC) content but lower soil pH generated higher peak voltage and charge. The sequencing of Fe(III)-reducing bacteria showed that Clostridia were dominant in all soil samples. At the family level, Clostridiales Family XI incertae sedis were dominant in soils with lower OC content but higher pH (>8), while Clostridiaceae, Lachnospiraceae, and Planococcaceae were dominant in soils with higher OC content but lower pH. The isolated culturable strains were allied phylogenetically to 15 different species, of which 11 were Clostridium. The others were Robinsoniella peoriensis, Hydrogenoanaerobacterium saccharovorans, Eubacterium contortum, and Oscillibacter ruminantium. The maximum power density generated by the isolates in the MFCs ranged from 16.4 to 28.6 mW m-2. We concluded that soil OC content had the most important effect on power generation and that the Clostridiaceae were the dominant exoelectrogenic bacterial group in soil. This study might lead to the discovery of more soil source exoelectrogenic bacteria species.

Inhibition of bacterial ammonia oxidation by organohydrazines in soil microcosms.

Hydroxylamine oxidation by hydroxylamine oxidoreductase (HAO) is a key step for energy-yielding in support of the growth of ammonia-oxidizing bacteria (AOB). Organohydrazines have been shown to inactivate HAO from Nitrosomonas europaea, and may serve as selective inhibitors to differentiate bacterial from archaeal ammonia oxidation due to the absence of bacterial HAO gene homolog in known ammonia-oxidizing archaea (AOA). In this study, the effects of three organohydrazines on activity, abundance, and composition of AOB and AOA were evaluated in soil microcosms. The results indicate that phenylhydrazine and methylhydrazine at the concentration of 100 μmol g−1 dry weight soil completely suppressed the activity of soil nitrification. Denaturing gradient gel electrophoresis fingerprinting and sequencing analysis of bacterial ammonia monooxygenase subunit A gene (amoA) clearly demonstrated that nitrification activity change is well paralleled with the growth of Nitrosomonas europaea-like AOB in soil microcosms. No significant correlation between AOA community structure and nitrification activity was observed among all treatments during the incubation period, although incomplete inhibition of nitrification activity occurred in 2-hydroxyethylhydrazine-amended soil microcosms. These findings show that the HAO-targeted organohydrazines can effectively inhibit bacterial nitrification in soil, and the mechanism of organohydrazine affecting AOA remains unclear.

Response of soil microbial diversity to land-use conversion of natural forests to plantations in a subtropical mountainous area of southern China

Land-use conversion can affect the soil microbial community diversity, soil organic matter and nutrient cycling. In this study, soils within a representative land-use sequence were sampled in a subtropical region of China, including four natural forests, Altingia gracilipes Hemsl. (ALG), Cinnamomum chekiangense Nakai (CIC), Castanopsis fargesii Franch. (CAF), and Tsoongiodendron odorum Chun (TSO), and two plantations, Cunninghamia lanceolata (Lamb.) Hook. (CUL) and a citrus orchard (Citrus reticulata Blanco). The soil microbial diversity was investigated by phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE) and real-time quantitative polymerase chain reaction (PCR). Results showed that microbial community diversity exhibited distinct patterns among land-use types. After conversion of natural forests to plantations, the amount of PLFA and the number of bacterial 16 S rRNA gene copies were reduced significantly, as well as the number of DGGE bands. The average quantity of PLFA was lower by 31% in the CUL plantation and 57% in the citrus orchard, respectively, than in natural forests. Simultaneously, the average copy numbers of the bacterial 16 S rRNA gene were significantly decreased from 8.1 × 1010 g−1 dry weight (DW) in natural forest to 4.9 × 1010 g−1 DW in CUL plantation, and 3.1 × 1010 g−1 DW in the citrus orchard. Such negative responses of soil microbes to conversion of natural forests to plantations could mainly result from decreases in soil organic carbon and necessary elements for growth during land-use conversion, as revealed by statistical analysis. Our results suggested that the soil microbial diversity was indirectly influenced by land-use types in the mid-subtropical mountainous area of southern China. Changes in the amount of litterfall and the soil nutrient status that resulted from land-use conversion drove these indirect changes. Furthermore, deliberate management brought negative effects on soil microbes, which is not beneficial to the sustainability of the ecosystem.

Long-term application of organic manure changes abundance and composition of ammonia-oxidizing archaea in an acidic red soil

Abstract Ammonia-oxidizing archaea (AOA) have more importance in ammonia oxidation than ammonia-oxidizing bacteria (AOB) in acidic red soils. The aim of this study was to investigate if the abundance and composition of AOA could be altered by long-term application of organic manure in an acidic red soil. The abundance and composition of AOA were evaluated by polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) targeting archaeal amoA genes after long-term (24-year) application of mineral fertilizer and/or organic manure. The treatments were: non-fertilized control, mineral nitrogen (N) fertilizer only, mineral N, phosphorus (P) and potassium (K) fertilizer only, organic manure only, and organic manure plus mineral NPK fertilizer. The abundance of archaeal amoA genes was significantly increased after the long-term application of organic manures, either with or without mineral NPK fertilizer. So were the Shannon and Richness diversity indices of AOA deduced from the DGGE patterns. Phylogenetic analyses showed that most of the AOA sequences from various fertilization treatments were affiliated with group 1.1b thaumarchaea and only one with the group 1.1a-associated thaumarchaea. Nitrification potential was significantly increased after the long-term application of organic manures in comparison with the non-fertilized control. Our results strengthened the importance of organic manure in promoting the growth of AOA and thus nitrification potential in the acidic red soils.

Effects of transgenic Bt rice on the active rhizospheric methanogenic archaeal community as revealed by DNA-based stable isotope probing

This study aimed to investigate the influence of planting Cry1Ab/Cry1Ac gene expressing rice (Bt rice) on rhizospheric active methanogenic archaeal communities.

Vertical distribution and community composition of anammox bacteria in sediments of a eutrophic shallow lake

The aim of this study was to explore the vertical distribution traits of anaerobic ammonium‐oxidizing (anammox) bacterial relative abundance and community composition along the oxic/anoxic sediment profiles in a shallow lake.