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.     

森林固碳释氧服务价值与异养呼吸损失量评估

固碳释氧是森林最重要的生态系统服务之一,将森林碳收支与固碳释氧服务价值评估相结合对于准确评估生态系统服务价值具有重要意义。应用森林碳收支模型(CBM-CFS3),分别基于净初级生产力(NPP)和净生态系统生产力(NEP)评估了2009—2030年湖北省兴山县森林生态系统总、净固碳释氧服务价值的时空动态,量化了异养呼吸造成的固碳释氧服务价值损失。模拟期间兴山县森林生态系统NPP逐渐增加(0.46—0.70 Tg/a),NEP由0.12 Tg/a先增加至0.21 Tg/a,然后逐渐下降至0.18 Tg/a;所对应的森林总、净固碳释氧服务价值范围分别为7.59—11.53亿元/a和2.21—3.70亿元/a。异养呼吸逐年增加,导致固碳释氧价值每年损失平均值为7.29亿元/a或4509元hm~(-2) a~(-1),约占总价值的68.6%。兴山县东南部异养呼吸造成的森林固碳释氧服务价值损失较高,而中部及西南部森林净固碳释氧价值较高。模拟期间兴山县森林为碳汇,稳定地提供固碳释氧服务。与NPP相比,使用NEP评估固碳释氧服务价值更为合理。忽视异养呼吸将严重高估森林生态系统固碳释氧服务价值;因而必须将物质循环过程与生态系统服务评估相结合,以降低评估结果的不确定性、提高生态系统服务的评估能力。     

A strategy for high cell density culture of heterotrophic microalgae with inhibitory substrates

Substrate inhibition is one of the major problems preventing high cell densities of microalgae in heterotrophic culture, so the possibility of overcoming the problem by various culture techniques was examined. It was found that perfusion culture may be the most appropriate technique for high cell densities in heterotrophic culture using inhibitory substrates. An experimental example in which a hollow fibre cell recycle system (HFCRS) was employed to achieve high cell densities of Chlamydomonas reinhardtii on acetate under heterotrophic conditions of growth was demonstrated. The cell density in the HFCRS was much higher than that reported in the literature for this species.     

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.     

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。     

Microbial community responses reduce soil carbon loss in Tibetan alpine grasslands under short‐term warming

Changes in labile carbon (LC) pools and microbial communities are the primary factors controlling soil heterotrophic respiration (R_h) in warming experiments. Warming is expected to initially increase R_h but studies show this increase may not be continuous or sustained. Specifically, LC and soil microbiome have been shown to contribute to the effect of extended warming on R_h. However, their relative contribution is unclear and this gap in knowledge causes considerable uncertainty in the prediction of carbon cycle feedbacks to climate change. In this study, we used a two‐step incubation approach to reveal the relative contribution of LC limitation and soil microbial community responses in attenuating the effect that extended warming has on R_h. Soil samples from three Tibetan ecosystems—an alpine meadow (AM), alpine steppe (AS), and desert steppe (DS)—were exposed to a temperature gradient of 5–25°C. After an initial incubation period, soils were processed in one of two methods: (a) soils were sterilized then inoculated with parent soil microbes to assess the LC limitation effects, while controlling for microbial community responses; or (b) soil microbes from the incubations were used to inoculate sterilized parent soils to assess the microbial community effects, while controlling for LC limitation. We found both LC limitation and microbial community responses led to significant declines in R_h by 37% and 30%, respectively, but their relative contributions were ecosystem specific. LC limitation alone caused a greater R_h decrease for DS soils than AMs or ASs. Our study demonstrates that soil carbon loss due to R_h in Tibetan alpine soils—especially in copiotrophic soils—will be weakened by microbial community responses under short‐term warming.