Xiao-Ru Yang

A marine algicidal actinomycete and its active substance against the harmful algal bloom species Phaeocystis globosa

A strain O4-6, which had pronounced algicidal effects to the harmful algal bloom causing alga Phaeocystis globosa, was isolated from mangrove sediments in the Yunxiao Mangrove National Nature Reserve, Fujian, China. Based on the 16S rRNA gene sequence and morphological characteristics, the isolate was found to be phylogenetically related to the genus Streptomyces and identified as Streptomyces malaysiensis O4-6. Heat stability, pH tolerance, molecular weight range and aqueous solubility were tested to characterize the algicidal compound secreted from O4-6. Results showed that the algicidal activity of this compound was not heat stable and not affected by pH changes. Residue extracted from the supernatant of O4-6 fermentation broth by ethyl acetate, was purified by Sephadex LH-20 column and silica gel column chromatography before further structure determination. Chemical structure of the responsible compound, named NIG355, was illustrated based on quadrupole time-of-flight mass spectrometry (Q-TOF-MS) and nuclear magnetic resonance (NMR) spectra. And this compound showed a stronger algicidal activity compared with other reported algicides. Furthermore, this article represents the first report of an algicide against P. globosa, and the compound may be potentially used as a bio-agent for controlling harmful algal blooms.

Potential Contribution of Anammox to Nitrogen Loss from Paddy Soils in Southern China

ABSTRACT The anaerobic oxidation of ammonium (anammox) process has been observed in diverse terrestrial ecosystems, while the contribution of anammox to N2 production in paddy soils is not well documented. In this study, the anammox activity and the abundance and diversity of anammox bacteria were investigated to assess the anammox potential of 12 typical paddy soils collected in southern China. Anammox bacteria related to “Candidatus Brocadia” and “Candidatus Kuenenia” and two novel unidentified clusters were detected, with “Candidatus Brocadia” comprising 50% of the anammox population. The prevalence of the anammox was confirmed by the quantitative PCR results based on hydrazine synthase (hzsB) genes, which showed that the abundance ranged from 1.16 × 104 to 9.65 × 104 copies per gram of dry weight. The anammox rates measured by the isotope-pairing technique ranged from 0.27 to 5.25 nmol N per gram of soil per hour in these paddy soils, which contributed 0.6 to 15% to soil N2 production. It is estimated that a total loss of 2.50 × 106 Mg N per year is linked to anammox in the paddy fields in southern China, which implied that ca. 10% of the applied ammonia fertilizers is lost via the anammox process. Anammox activity was significantly correlated with the abundance of hzsB genes, soil nitrate concentration, and C/N ratio. Additionally, ammonia concentration and pH were found to be significantly correlated with the anammox bacterial structure.

Diversity and Abundance of Arsenic Biotransformation Genes in Paddy Soils from Southern China

Microbe-mediated arsenic (As) biotransformation in paddy soils determines the fate of As in soils and its availability to rice plants, yet little is known about the microbial communities involved in As biotransformation. Here, we revealed wide distribution, high diversity, and abundance of arsenite (As(III)) oxidase genes (aioA), respiratory arsenate (As(V)) reductase genes (arrA), As(V) reductase genes (arsC), and As(III) S-adenosylmethionine methyltransferase genes (arsM) in 13 paddy soils collected across Southern China. Sequences grouped with As biotransformation genes are mainly from rice rhizosphere bacteria, such as some Proteobacteria, Gemmatimonadales, and Firmicutes. A significant correlation of gene abundance between arsC and arsM suggests that the two genes coexist well in the microbial As resistance system. Redundancy analysis (RDA) indicated that soil pH, EC, total C, N, As, and Fe, C/N ratio, SO4(2-)-S, NO3(-)-N, and NH4(+)-N were the key factors driving diverse microbial community compositions. This study for the first time provides an overall picture of microbial communities involved in As biotransformation in paddy soils, and considering the wide distribution of paddy fields in the world, it also provides insights into the critical role of paddy fields in the As biogeochemical cycle.

Nitrogen loss by anaerobic oxidation of ammonium in rice rhizosphere

Anaerobic oxidation of ammonium (anammox) is recognized as an important process for nitrogen (N) cycling, yet its role in agricultural ecosystems, which are intensively fertilized, remains unclear. In this study, we investigated the presence, activity, functional gene abundance and role of anammox bacteria in rhizosphere and non-rhizosphere paddy soils using catalyzed reporter deposition–fluorescence in situ hybridization, isotope-tracing technique, quantitative PCR assay and 16S rRNA gene clone libraries. Results showed that rhizosphere anammox contributed to 31–41% N2 production with activities of 0.33–0.64 nmol N2 g−1 soil h−1, whereas the non-rhizosphere anammox bacteria contributed to only 2–3% N2 production with lower activities of 0.08–0.26 nmol N2 g−1 soil h−1. Higher anammox bacterial cells were observed (0.75–1.4 × 107 copies g−1 soil) in the rhizosphere, which were twofold higher compared with the non-rhizosphere soil (3.7–5.9 × 106 copies g−1 soil). Phylogenetic analysis of the anammox bacterial 16S rRNA genes indicated that two genera of ‘Candidatus Kuenenia’ and ‘Candidatus Brocadia’ and the family of Planctomycetaceae were identified. We suggest the rhizosphere provides a favorable niche for anammox bacteria, which are important to N cycling, but were previously largely overlooked.

Electron Shuttles Enhance Anaerobic Ammonium Oxidation Coupled to Iron(III) Reduction

Anaerobic ammonium oxidation coupled to iron(III) reduction, termed Feammox, is a newly discovered nitrogen cycling process. However, little is known about the roles of electron shuttles in the Feammox reactions. In this study, two forms of Fe(III) (oxyhydr)oxide ferrihydrite (ex situ ferrihydrite and in situ ferrihydrite) were used in dissimilatory Fe(III) reduction (DIR) enrichments from paddy soil. Evidence for Feammox in DIR enrichments was demonstrated using the (15)N-isotope tracing technique. The extent and rate of both the (30)N2-(29)N2 and Fe(II) formation were enhanced when amended with electron shuttles (either 9,10-anthraquinone-2,6-disulfonate (AQDS) or biochar) and further simulated when these two shuttling compounds were combined. Although the Feammox-associated Fe(III) reduction accounted for only a minor proportion of total Fe(II) formation compared to DIR, it was estimated that the potentially Feammox-mediated N loss (0.13-0.48 mg N L(-1) day(-1)) was increased by 17-340% in the enrichments by the addition of electron shuttles. The addition of electron shuttles led to an increase in the abundance of unclassified Pelobacteraceae, Desulfovibrio, and denitrifiers but a decrease in Geobacter. Overall, we demonstrated a stimulatory effect of electron shuttles on Feammox that led to higher N loss, suggesting that electron shuttles might play a crucial role in Feammox-mediated N loss from soils.

Novel insights into the algicidal bacterium DH77-1 killing the toxic dinoflagellate Alexandrium tamarense

Algicidal bacteria may play a major role in controlling harmful algal blooms (HABs) dynamics. Bacterium DH77-1 was isolated with high algicidal activity against the toxic dinoflagellate Alexandrium tamarense and identified as Joostella sp. DH77-1. The results showed that DH77-1 exhibited algicidal activity through indirect attack, which excreted active substance into the filtrate. It had a relatively wide host range and the active substance of DH77-1 was relatively stable since temperature, pH and storage condition had no obvious effect on the algicidal activity. The algicidal compound from bacterium DH77-1 was isolated based on activity-guided bioassay and the molecular weight was determined to be 125.88 by MALDI-TOF mass spectrometer, however further identification via nuclear magnetic resonance (NMR) spectra is ongoing. The physiological responses of algal cells after exposure to the DH77-1 algicidal substances were as follows: the antioxidant system of A. tamarense responded positively in self-defense; total protein content decreased significantly as did the photosynthetic pigment content; superoxide dismutase, peroxidase enzyme and malondialdehyde content increased extraordinarily and algal cell nucleic acid leaked seriously ultimately inducing cell death. Furthermore, DH77-1 is the first record of a Joostella sp. bacterium being algicidal to the harmful dinoflagellate A. tamarense, and the bacterial culture and the active compounds might be potentially used as a bio-agent for controlling harmful algal blooms.

Insights into the role of plant on ammonia-oxidizing bacteria and archaea in the mangrove ecosystem

PurposeThe aim of this study was to elucidate the impact of plant on the activity, abundance, and the community composition of the ammonia oxidizers, including both ammonia-oxidizing archaea (AOA) and bacteria (AOB). Moreover, the relationship between AOA and AOB in mangrove sediment was also analyzed.Materials and methodsSediment used for microcosm experiments was collected in the mangrove wetland. The native plant species Kandelia obovata and invasive species Spartina alterniflora were selected. Nitrifying activity was determined by assaying the potential nitrification rate (PNR). Abundances of gene and transcript were measured via real-time quantitative PCR (qPCR). Terminal restriction fragment length polymorphism (T-RFLP) was used to analyze the nitrifier community structures. Clone libraries were constructed for further phylogenetic analysis.Results and discussionPNR and abundances of both AOA and AOB were greatly enhanced in the vegetated sediments. S. alterniflora showed a greater promoting effect on nitrification activity, indicating the potential of exotic invasion on perturbing the nitrogen balance. Abundance of AOB transcript was hundreds of times higher than that of AOA. Moreover, ammonia-oxidizing communities were distinctly grouped responding to vegetation with two plant species. Along with direct impact of plants, these variations are as well related to the different sediment properties. Phylogenetic analysis revealed that both AOA and AOB communities formed apparent clusters. The latter contained two Nitrosomonas and Nitrosospira clusters. The Nitrosomonas genus is predominant over Nitrosospira genus, which might be due to the better adaption of Nitrosomonas to the flooded habitats in sediments.ConclusionsWetland plants were found to influence the activity, abundance, and community structure of ammonia oxidizers. Moreover, AOB is suggested to be more significant than AOA in nitrogen cycling in mangrove wetlands.

Phaeocystidibacter luteus gen nov, sp nov, a member of the family Cryomorphaceae isolated from the marine alga Phaeocystis globosa, and emended description of Owenweeksia hongkongensis

A taxonomic study was carried out on strain PG2S01(T), isolated from a culture of Phaeocystis globosa, a haemolytic, toxin-producing, harmful marine alga. Cells of strain PG2S01(T) were Gram-negative, strictly aerobic, non-motile, non-fermentative, orange-pigmented, moderately halophilic rods. Growth was observed in the presence of 0.25-7.5 % NaCl and at 10-40 °C. The dominant fatty acids were iso-C15 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c), iso-C17 : 0 3-OH, iso-C16 : 0 3-OH, iso-C15 : 1 G and iso-C15 : 0 3-OH. The major polar lipids were phosphatidylethanolamine and several unidentified aminolipids, phospholipids and other lipids. The G+C content of the chromosomal DNA was 44.6 mol%. 16S rRNA gene sequence comparison showed that strain PG2S01(T) was most closely related to Owenweeksia hongkongensis UST20020801(T) (88.9 % 16S rRNA gene sequence similarity); levels of similarity between strain PG2S01(T) and the type strains of recognized representatives of genera in the family Cryomorphaceae were <88 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain PG2S01(T) formed a distinct evolutionary lineage within the family Cryomorphaceae. Strain PG2S01(T) was distinguishable from members of phylogenetically related genera by differences in several phenotypic properties. On the basis of phenotypic data and phylogenetic inference, strain PG2S01(T) represents a novel species in a new genus in the family Cryomorphaceae, for which the name Phaeocystidibacter luteus gen. nov., sp. nov. is proposed. The type strain of the type species is PG2S01(T) ( = CCTCC AB 209288(T)  = LMG 25704(T)  = MCCC 1F01079(T)). An emended description of O. hongkongensis Lau et al. 2005 is also proposed.

Changes in land use driven by urbanization impact nitrogen cycling and the microbial community composition in soils

Transition of populations from rural to urban living causes landscape changes and alters the functionality of soil ecosystems. It is unclear how this urbanization disturbs the microbial ecology of soils and how the disruption influences nitrogen cycling. In this study, microbial communities in turfgrass-grown soils from urban and suburban areas around Xiamen City were compared to microbial communities in the soils from rural farmlands. The potential N2O emissions, potential denitrification activity, and abundances of denitrifiers were higher in the rural farmland soils compared with the turfgrass soils. Ammonia oxidizing archaea (AOA) were more abundant than ammonia oxidizing bacteria (AOB) in turfgrass soils. Within turfgrass soils, the potential nitrification activities and AOA abundances were higher in the urban than in the suburban soils. These results indicate a more pivotal role of AOA in nitrification, especially in urban soils. Microbial community composition was distinctly grouped along urbanization categories (urban, suburban, and rural) classified according to the population density, which can in part be attributed to the differences in soil properties. These observed changes could potentially have a broader impact on soil nutrient availability and greenhouse gas emissions.

Long-term effect of temperature on N2O emission from the denitrifying activated sludge

The long-term effect of various temperature (4°C, 12°C, 20°C, 25°C and 34°C) on nitrous oxide (N2O) emission from lab-scale denitrifying activated sludge was studied in terms of activation energy, abundance of functional gene nosZ and its transcription. Results showed that temperature had a positive effect on N2O emissions as well as the maximum biomass-specific reduction rates of N2O and NO3(-), ranging from 0.006% to 0.681% of (N2O + N2), 17.3-116.2 and 5.2-66.2 mg N g(-1) VSS h(-1), respectively. The activation energies (Ea) for N2O and NO3(-) reduction of 44.1 kJ mol(-1) and 54.9 kJ mol(-1), shed light on differences in denitrifying rate variation. The maximum NO3(-) reduction rates were more sensitive to temperature variation than the corresponding N2O reduction rates under long-term acclimation. As a result, the ratio between N2O and NO3(-) reduction rates declined to 1.87 at 34°C from 3.31 at 4°C, suggesting great potential capacity for N2O losses at high temperature. The copy numbers of denitrifiers as nosZ gene (×10(8) copies mL(-1)) and total bacteria as 16S rRNA gene (×10(10) copies mL(-1)) did not show obvious relationship with temperature, having relative abundance of 0.42% on average. The transcriptional regulation of nosZ gene, in the range of 10(8)-10(5) copies mL(-1), was affected by reductase activity, substrate concentration as well as its duration. The active nosZ gene expression was accompanied with low reductase capacity, high dissolved N2O and the duration of N2O accumulation. These results provide insights into activation energy and gene expression responsible for N2O emission.