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

Effect of salt stress on aerobic methane oxidation and associated methanotrophs; a microcosm study of a natural community from a non-saline environment

We investigated the response of aerobic methane oxidation and the associated methanotrophs to salt-stress in a NaCl gradient ranging from 0 M (un-amended reference) to 0.6 M NaCl (seawater salinity) using a rice paddy soil as a model system. Salt-stress significantly inhibited methanotrophic activity at > 0.3 M NaCl at 0.6 M NaCl amendment, methanotrophic activity fully ceased. MiSeq sequencing of the pmoA gene and group-specific qPCR analyses revealed that type Ia methanotroph (Methylobacter) appeared to be favored under salinity up to 0.3 M NaCl, increasing in numerical abundance, while the type Ib was adversely affected. This suggests niche differentiation within members of the gammaproteobacterial methanotrophs. Overall, rice paddy soil methanotrophs showed remarkable resistance to salt-stress

Robust Optimization of Fourth Party Logistics Network Design under Disruptions

The Fourth Party Logistics (4PL) network faces disruptions of various sorts under the dynamic and complex environment. In order to explore the robustness of the network, the 4PL network design with consideration of random disruptions is studied. The purpose of the research is to construct a 4PL network that can provide satisfactory service to customers at a lower cost when disruptions strike. Based on the definition of β-robustness, a robust optimization model of 4PL network design under disruptions is established. Based on the NP-hard characteristic of the problem, the artificial fish swarm algorithm (AFSA) and the genetic algorithm (GA) are developed. The effectiveness of the algorithms is tested and compared by simulation examples. By comparing the optimal solutions of the 4PL network for different robustness level, it is indicated that the robust optimization model can evade the market risks effectively and save the cost in the maximum limit when it is applied to 4PL network design

Disentangling abiotic and biotic controls of aerobic methane oxidation during re-colonization

Aerobic methane oxidation is driven by both abiotic and biotic factors, which are often confounded in the soil environment. Using a laboratory-scale reciprocal inoculation experiment with two native soils (paddy and upland agricultural soils) and the gamma-irradiated fraction of these soils, we aim to disentangle and determine the relative contribution of abiotic (i.e., soil edaphic properties) and biotic (i.e., initial methanotrophic community composition) controls of methane oxidation during re-colonization. Methane uptake was appreciably higher in incubations containing gamma-irradiated paddy than upland soil despite the initial difference in the methanotrophic community composition. This suggested an overriding effect of the soil edaphic properties, which positively regulated methane oxidation. Community composition was similar in incubations with the same starting inoculum, based on quantitative and qualitative pmoA gene analyses. Thus, results suggested that the initial community composition affects the trajectory of community succession to an extent, but not at the expense of the methanotrophic activity under high methane availability. Still, methane oxidation was affected more by soil edaphic properties than by the initial composition of the methanotrophic community

When the going gets tough: Emergence of a complex methane-driven interaction network during recovery from desiccation-rewetting

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 disturbances, and how community functioning is affected by the disturbance-induced structuring of the interaction network. Here, we employed a time-series stable isotope probing (SIP) approach using 13C–CH4 coupled to a co-occurrence network analysis after Illumina MiSeq sequencing of the 13C-enriched 16S rRNA gene to directly relate the response in methanotrophic activity to the network structure of the interactome after desiccation-rewetting of a paddy soil. Methane uptake rate decreased immediately (<5 days) after short-term desiccation-rewetting. Although the methanotroph subgroups differentially responded to desiccation-rewetting, the metabolically active bacterial community composition, including the methanotrophs, recovered after the disturbance. However, the interaction network was profoundly altered, becoming more complex but, less modular after desiccation-rewetting, despite the recovery in the methanotrophic activity and community composition/abundances. This suggests that the legacy of the disturbance persists in the interaction network. The change in the network structure may have consequences for community functioning with recurring desiccation-rewetting

Long-Term Adaptation of Acidophilic Archaeal Ammonia Oxidisers Following Different Soil Fertilisation Histories

Acknowledgements We thank Prof Yuanqiu He (now deceased) at the State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences for his contribution to this study. In addition, we thank the staff of the Analysis Center at the Institute of Soil Science for technical support, including Ms Rong Huang and Mr Zuohao Ma for 454-pyrosequencing, Mr Ruhai Wang for the ammonia and nitrate and nitrite content assays, Mr Guoxing Lu for the SOM assay. We also thank Dr Jian Cui and Dr Xiaoli Liu for assistance in soil sampling in the fields. Funding This work was supported by the National Natural Science Foundation of China (41530857, 91751204 and 41977056). JZ was funded by a Natural Environment Research Council grant (NE/K016342/1) and CGR was supported by a Royal Society University Research Fellowship (URF150571).Peer reviewedPublisher PD

Biotic interactions in microbial communities as modulators of biogeochemical processes : methanotrophy as a model system

Microbial interaction is an integral component of microbial ecology studies, yet the role, extent, and relevance of microbial interaction in community functioning remains unclear, particularly in the context of global biogeochemical cycles. While many studies have shed light on the physico-chemical cues affecting specific processes, (micro)biotic controls and interactions potentially steering microbial communities leading to altered functioning are less known. Yet, recent accumulating evidence suggests that the concerted actions of a community can be significantly different from the combined effects of individual microorganisms, giving rise to emergent properties. Here, we exemplify the importance of microbial interaction for ecosystem processes by analysis of a reasonably well-understood microbial guild, namely, aerobic methane-oxidizing bacteria (MOB). We reviewed the literature which provided compelling evidence for the relevance of microbial interaction in modulating methane oxidation. Support for microbial associations within methane-fed communities is sought by a re-analysis of literature data derived from stable isotope probing studies of various complex environmental settings. Putative positive interactions between active MOB and other microbes were assessed by a correlation network-based analysis with datasets covering diverse environments where closely interacting members of a consortium can potentially alter the methane oxidation activity. Although, methanotrophy is used as a model system, the fundamentals of our postulations may be applicable to other microbial guilds mediating other biogeochemical processes

Grazing weakens competitive interactions between active methanotrophs and nitrifiers modulating greenhouse-gas emissions in grassland soils

This work was financially supported by Natural Science Foundation of China (41977033, 41907026, and 41721001), Fundamental Research Funds for the Central Universities (2019QNA6011), National Key Basic Research Program of China (2014CB138801), Shandong Provincial Natural Science Foundation (ZR2019BD032), China Postdoctoral Science Foundation (2020T130387 and 2019M652448). CG-R was funded by a Royal Society University Research Fellowship (UF150571). Special thanks to ChunMei Meng, Yu Luo, and Yan Zheng for their assistance in laboratory analyses.Peer reviewedPublisher PD

Combined effects of temperature and dietary lipid level on body composition, growth, and freshness profile in european seabass, dicentrarchus labrax

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 index than those reared at 20 °C. On the other hand, the sea bass condition index did not change among treatments. Additionally, sensory analysis (the Quality Index Method) and microbiological analysis revealed that fish reared at 24 °C showed better freshness conditions than those at 20 °C. Nevertheless, the dietary lipid level did not have any influence on fish freshness conditions. Therefore, our data suggest that the increase in temperature to 24 °C is beneficial for the growth and freshness profile of this particular species in aquaculture.info:eu-repo/semantics/publishedVersio

Expansion of Thaumarchaeota habitat range is correlated with horizontal transfer of ATPase operons.

Thaumarchaeota are responsible for a significant fraction of ammonia oxidation in the oceans and in soils that range from alkaline to acidic. However, the adaptive mechanisms underpinning their habitat expansion remain poorly understood. Here we show that expansion into acidic soils and the high pressures of the hadopelagic zone of the oceans is tightly linked to the acquisition of a variant of the energy-yielding ATPases via horizontal transfer. Whereas the ATPase genealogy of neutrophilic Thaumarchaeota is congruent with their organismal genealogy inferred from concatenated conserved proteins, a common clade of V-type ATPases unites phylogenetically distinct clades of acidophilic/acid-tolerant and piezophilic/piezotolerant species. A presumptive function of pumping cytoplasmic protons at low pH is consistent with the experimentally observed increased expression of the V-ATPase in an acid-tolerant thaumarchaeote at low pH. Consistently, heterologous expression of the thaumarchaeotal V-ATPase significantly increased the growth rate of E. coli at low pH. Its adaptive significance to growth in ocean trenches may relate to pressure-related changes in membrane structure in which this complex molecular machine must function. Together, our findings reveal that the habitat expansion of Thaumarchaeota is tightly correlated with extensive horizontal transfer of atp operons