Single-cell genomics shedding light on marine Thaumarchaeota diversification

Previous studies based on analysis of amoA, 16S ribosomal RNA or accA gene sequences have established that marine Thaumarchaeota fall into two phylogenetically distinct groups corresponding to shallow- and deep-water clades, but it is not clear how water depth interacts with other environmental factors, including light, temperature and location, to affect this pattern of diversification. Earlier studies focused on single-gene distributions were not able to link phylogenetic structure to other aspects of functional adaptation. Here, we analyzed the genome content of 46 uncultivated single Thaumarchaeota cells sampled from epi- and mesopelagic waters of subtropical, temperate and polar oceans. Phylogenomic analysis showed that populations diverged by depth, as expected, and that mesopelagic populations from different locations were well mixed. Functional analysis showed that some traits, including putative DNA photolyase and catalase genes that may be related to adaptive mechanisms to reduce light-induced damage, were found exclusively in members of the epipelagic clade. Our analysis of partial genomes has thus confirmed the depth differentiation of Thaumarchaeota populations observed previously, consistent with the distribution of putative mechanisms to reduce light-induced damage in shallow- and deep-water populations.     

Enrichment and characterization of ammonia-oxidizing archaea from the open ocean: phylogeny,physiology and stable isotope fractionation

Archaeal genes for ammonia oxidation are widespread in the marine environment, but direct physiological evidence for ammonia oxidation by marine archaea is limited. We report the enrichment and characterization of three strains of pelagic ammonia-oxidizing archaea (AOA) from the North Pacific Ocean that have been maintained in laboratory culture for over 3 years. Phylogenetic analyses indicate the three strains belong to a previously identified clade of water column-associated AOA and possess 16S ribosomal RNA genes and ammonia monooxygenase subunit a (amoA) genes highly similar (98–99% identity) to those recovered in DNA and complementary DNA clone libraries from the open ocean. The strains grow in natural seawater-based liquid medium while stoichiometrically converting ammonia (NH₃) to nitrite (NO₂⁻). Ammonia oxidation by the enrichments is only partially inhibited by allylthiourea at concentrations known to completely inhibit cultivated ammonia-oxidizing bacteria. The three strains were used to determine the nitrogen stable isotope effect (¹⁵ɛ_NH3) during archaeal ammonia oxidation, an important parameter for interpreting stable isotope ratios in the environment. Archaeal ¹⁵ɛ_NH3 ranged from 13‰ to 41‰, within the range of that previously reported for ammonia-oxidizing bacteria. Despite low amino acid identity between the archaeal and bacterial Amo proteins, their functional diversity as captured by ¹⁵ɛ_NH3 is similar.     

The effect of sodium chlorate and nitrapyrin on the nitrification mediated nitrosation process in soils

Summary The influence of total nitrification to nitrate or partial nitrification to nitrite on the soil organic nitrogen status was examined. NH ₄ ⁺ –¹⁵N was added to the soil in the absence and the presence of NaClO₃, respectively nitrapyrin. The first chemical inhibits only nitrate formation, the second inhibits total nitrification. The accumulation of nitrite nitrogen in the soil at levels up to 5 mg kg^–1 increased the loss of nitrogen. Yet, it did not increase the binding of mineral nitrogen into soil organic matter, relative to the control soil. The data suggest that the biochemistry of the nitrite formation process, rather than the levels of nitrite ions formed, are of primary importance in the role of nitrification mediated nitrosation of soil organic matter.     

恩诺沙星残留对土壤微生物功能的影响

研究了恩诺沙星残留对土壤呼吸作用、纤维分解作用、氨化作用、硝化作用的影响 ,结果表明 ,相对较低浓度恩诺沙星残留(0 .0 1μg/ g土 ,0 .1μg/ g土 )刺激土壤呼吸作用 ,相对较高浓度恩诺沙星残留 (1μg/ g土 )对土壤呼吸作用产生抑制 ,药物作用活性维持期为 6 d;恩诺沙星残留对土壤纤维分解作用影响较不明显 ;较低浓度恩诺沙星残留 (0 .0 1μg/ g土 ,0 .1μg/ g土 )对土壤氨化作用有刺激作用 ,而较高浓度恩诺沙星残留 (1μg/ g土 ,10μg/ g土 )则会对其起抑制作用 ,药物作用活性期为 9d;不同浓度恩诺沙星对土壤硝化作用影响极其显著 ,当恩诺沙星浓度达到 1μg/ ml时 ,在 3～ 9d内 ,对土壤硝化作用有一定抑制作用。当恩诺沙星浓度达到 10μg/ ml时 ,强烈抑制了土壤硝化作用 ,直到本试验结束时 ,其抑制作用未见减弱。结果表明恩诺沙星残留影响了土壤微生物这些功能 ,因而可能影响到土壤特性和土壤中一些生态过程     

Plant invasion alters nitrogen cycling by modifying the soil nitrifying community

Plant invasions have dramatic aboveground effects on plant community composition, but their belowground effects remain largely uncharacterized. Soil microorganisms directly interact with plants and mediate many nutrient transformations in soil. We hypothesized that belowground changes to the soil microbial community provide a mechanistic link between exotic plant invasion and changes to ecosystem nutrient cycling. To examine this possible link, monocultures and mixtures of exotic and native species were maintained for 4 years in a California grassland. Gross rates of nitrogen (N) mineralization and nitrification were quantified with ¹⁵N pool dilution and soil microbial communities were characterized with DNA‐based methods. Exotic grasses doubled gross nitrification rates, in part by increasing the abundance and changing the composition of ammonia‐oxidizing bacteria in soil. These changes may translate into altered ecosystem N budgets after invasion. Altered soil microbial communities and their resulting effects on ecosystem processes may be an invisible legacy of exotic plant invasions.     

Responses of Active Ammonia Oxidizers to Eutrophication and Oxygen Statuses in Taihu Freshwater Sediments

Abstract

Here, we employed DNA-based stable isotope probing (SIP) and molecular biology methods to investigate active ammonia oxidizer communities in suboxic sediments (0 to –2?cm) at the micromolar oxygen level and layers (–2 to –5?cm) at nanomolar oxygen concentrations from meso-eutrophic and light-eutrophic locations in Taihu Lake. The results revealed that ammonia-oxidizing archaea (AOA) were less active in the anoxic layer of meso-eutrophic sites, while ammonia-oxidizing bacteria (AOB) were less active in suboxic sediments of light-eutrophic sites after 8?weeks of incubation. The active AOA in the meso- and light-eutrophic sediments belonged to the Nitrosopumilus, Nitrosotalea, and Nitrososphaera clusters and the Nitrosopumilus and Nitrososphaera clusters, respectively, with Nitrosopumilus cluster as the predominant AOA, which took up a higher ratio in the light-eutrophic and suboxic layers than their counterparts. The advantageous active AOB were numerically predominated by the Nitrosomonas cluster in the suboxic layers, and the Nitrosospira cluster in the anoxic layers, respectively, both of which were distributed in diverse frequencies in different eutrophication statuses. The role and community composition diversities of active ammonia oxidizers in freshwater sediments were attributed to the different eutrophication (including nitrogen and organic carbon content) and oxygen statuses.     

Nitrification in hybrid bioreactors treating simulated domestic wastewater

Aim

To provide deeper insights into nitrification process within aerobic bioreactors containing supplemental physical support media (hybrid bioreactors).

Methods and Results

Three bench‐scale hybrid bioreactors with different media size and one control bioreactor were operated to assess how biofilm integrity influences microbial community conditions and bioreactor performance. The systems were operated initially at a 5‐day hydraulic retention time (HRT), and all reactors displayed efficient nitrification and chemical oxygen demand (COD) removal (>95%). However, when HRT was reduced to 2·5 days, COD removal rates remained high, but nitrification efficiencies declined in all reactors after 19 days. To explain reduced performance, nitrifying bacterial communities (ammonia‐oxidizing bacteria, AOB; nitrite‐oxidizing bacteria, NOB) were examined in the liquid phase and also on the beads using qPCR, FISH and DGGE. Overall, the presence of the beads in a reactor promoted bacterial abundances and diversity, but as bead size was increased, biofilms with active coupled AOB–NOB activity were less apparent, resulting in incomplete nitrification.

Conclusions

Hybrid bioreactors have potential to sustain effective nitrification at low HRTs, but support media size and configuration type must be optimized to ensure coupled AOB and NOB activity in nitrification.

Significance and Impact of the Study

This study shows that AOB and NOB coupling must be accomplished to minimize nitrification failure.     

川西亚高山不同森林类型土壤呼吸和总硝化速率的季节动态

川西亚高山原始林及其采伐后通过不同恢复措施形成的不同类型森林土壤呼吸和总硝化速率的对比分析及其耦合关系的研究相对匮乏。采用气压过程分离系统(Ba PS)技术研究了川西亚高山岷江冷杉原始林及其砍伐后恢复的粗枝云杉阔叶林、红桦-岷江冷杉天然次生林和粗枝云杉人工林土壤呼吸和总硝化速率的季节动态及其影响因素。结果表明:生长季内平均土壤呼吸速率和总硝化速率分别以粗枝云杉阔叶林和粗枝云杉人工林较高,均以岷江冷杉原始林较低。土壤呼吸和总硝化速率在生长季内具有明显的季节动态,呈以7月份最高的单峰趋势。土壤呼吸和总硝化速率与土壤温度显著相关,而与土壤水分相关性不显著,表明土壤温度是调控呼吸和总硝化作用季节动态的主要因子。土壤呼吸的温度敏感性(Q_(10))介于2.59—4.71,以岷江冷杉原始林最高,表明高海拔的岷江冷杉原始林可能更易受到气候变化的影响。林型间土壤呼吸和总硝化速率主要受凋落物量、p H和有机质的影响。不同林型间土壤呼吸和总硝化速率显著正相关,表明土壤呼吸和总硝化速率存在耦合关系。     

微生态制剂对海水养殖系统硝化功能建立过程的影响

比较分析投加不同微生态制剂的海水养殖系统硝化功能建立的过程,为实际应用提供依据。利用海水素构建4个海水养殖系统,通过投加硝化细菌、光合细菌、枯草芽胞杆菌3种微生态制剂以及纤维毛球作为生物膜载体,比较分析不同养殖系统硝化功能的建立过程及硝化强度差异。投加硝化细菌+光合细菌和硝化细菌+枯草芽胞杆菌系统硝化功能建立时间分别为108 h和96 h,氨氮初始质量浓度为6 mg/L时,氨氧化强度分别为1.69 mg/(L·d)和1.36 mg/(L·d);添加纤维毛球的生物膜系统与生物絮团系统硝化功能建立时间分别为96 h和120 h,氨氮初始质量浓度为6 mg/L时,氨氧化强度分别为1.36 mg/(L·d)和0.98 mg/(L·d);投加碳源系统和对照系统硝化功能建立时间分别为84 h和96 h,氨氮初始质量浓度为6 mg/L时,氨氧化强度分别为1.18 mg/(L·d)和1.36 mg/(L·d)。硝化细菌+枯草芽胞杆菌系统硝化功能建立时间更短,但系统硝化强度低于硝化细菌+光合细菌系统;生物膜系统硝化强度高于生物絮团系统且硝化功能建立更快;添加碳源能够加快系统硝化功能建立过程,但降低了硝化细菌+枯草芽胞杆菌系统的硝化强度。