The oxidation of ammonia to nitrite, which constitutes the initial and rate-limiting step in the nitrification process, plays a pivotal role in the transformation of ammonia within soil ecosystems. Due to its susceptibility to a range of pollutants, such as heavy metals, pesticides, and pharmaceuticals, nitrification serves as a valuable indicator in the risk assessment of chemical contaminants in soil environments. Here, we analyzed the effects of cadmium (Cd) treatment on soil potential nitrification rate (PNR), and the abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) communities. The results showed that, under 1 day incubation, the soil PNR with Cd 0.5 mg kg(-1) was a little higher but not statistically significant than that with zero mg kg(-1). Then, the soil PNR increased with the increasing Cd concentration from 0.5 to one mg kg(-1), and continuously declined from 1 to 10 mg kg(-1). Moreover, we predicted the bacterial functions of samples with hormetic Cd dose (one mg kg(-1)) by PICURSt (Phylogenetic Investigation of Communities Reconstruction of Unobserved States), and found that the expression of protein disulfide isomerase (PDI) increased with the hormetic Cd dose. PDI is known to enhance the activity of compounds containing -SH or -S-S which can help prevent oxidative damage to membranes. The soil PNR was significantly correlated with AOA abundance rather than AOB, even the abundance of AOB was higher than that of AOA, indicating that AOA functionally predominated over AOB. Our study effectively evaluated the Cd toxicity on soil microbial community and clearly illustrated the ecological niches of AOA and AOB in the agricultural soil system studied, which will be instructive for the sustainable development of agriculture.

Mining has led to dramatic ecosystem degradation, the destruction of vegetation and irreversible damage to soil structure and nutrient cycling; additionally, heavy metal (HM) contamination has affected soil nitrogen (N) cycle-associated microorganisms and disrupted soil aggregate structure. To explore the mechanism of soil N recovery in mining areas, we investigated the effects of two N fertilizers (urea (U) and ammonium chloride (AC)) and nine different fertilization patterns on the nitrification process and ammonia oxidizers in soil aggregates via incubation experiments. The results showed that different N treatments had different influences on the distribution of AOA and AOB amoA gene abundance and microbial community structure in soil aggregates. The AOB amoA gene abundance was significantly greater than the AOA amoA gene abundance in aggregates. The dominant species of AOA and AOB were Nitrososphaera and Nitrosospira , respectively, which were mainly found in microaggregates and accounted for 10.3 % to 25.0 % and 31.5 % to 60.1 %, respectively, of the microaggregates. Dissolved organic nitrogen (DON) can be used as an important variable to explain variations in AOA communities, and microbial nitrogen (MBN) content, tartaric acid content, cellulase activity and AOB amoA gene abundance can be used as important variables to explain variations in AOB communities. N fertilizer addition resulted in potential ammonia oxidation (PAO) values ranging from 0.079 to 0.236, 0.100 to 0.5953 and 0.146 to 0.905 mu g.NO2--N d(-1) g(-1) in mega-, macro- and microaggregates, respectively, which suggested that PAO values increased with decreasing aggregate size. In addition, the total nitrification potential (TNP) in macroaggregates was greater than that in mega- and microaggregates, which was the main reason for the increase in the NO3 content in macroaggregates. AOB amoA gene abundance was significantly positively correlated with TNP, and AOB amoA gene abundance was more significantly positively correlated with PAO values than was AOA gene abundance, which suggests that AOB dominated ammonia oxidation and nitrification processes in aggregates. Our research contributes to an understanding of the mechanisms underlying the effects of different types of N fertilizers on nitrification processes and ammonia oxidizers in soil aggregates and provides insights into N management in contaminated soils in mining areas.

Microbes are a critical component of soil ecosystems, performing crucial functions in biogeochemical cycling, carbon sequestration, and plant health. However, it remains uncertain how their community structure, functioning, and resul-tant nutrient cycling, including net GHG fluxes, would respond to climate change at different scales. Here, we review global and regional climate change effects on soil microbial community structure and functioning, as well as the climate-microbe feedback and plant-microbe interactions. We also synthesize recent studies on climate change impacts on terrestrial nutrient cycles and GHG fluxes across different climate-sensitive ecosystems. It is generally assumed that climate change factors (e.g., elevated CO2 and temperature) will have varying impacts on the microbial community structure (e.g., fungi-to-bacteria ratio) and their contribution toward nutrient turnover, with potential interactions that may either enhance or mitigate each other's effects. Such climate change responses, however, are difficult to gen-eralize, even within an ecosystem, since they are subjected to not only a strong regional influence of current ambient environmental and edaphic conditions, historical exposure to fluctuations, and time horizon but also to methodolog-ical choices (e.g., network construction). Finally, the potential of chemical intrusions and emerging tools, such as ge-netically engineered plants and microbes, as mitigation strategies against global change impacts, particularly for agroecosystems, is presented. In a rapidly evolving field, this review identifies the knowledge gaps complicating assessments and predictions of microbial climate responses and hindering the development of effective mitigation strategies.

Methane production in thawing permafrost can be substantial, yet often evolves after long lag phases or is even lacking. A central question is to which extent the production of methane after permafrost thaw is determined by the initial methanogenic community. We quantified the production of methane relative to carbon dioxide (CO2) and enumerated methanogenic (mcrA) gene copies in long-term (2-7 years) anoxic incubations at 4 degrees C using interglacial and glacial permafrost samples of Holocene and Pleistocene, including Eemian, origin. Changes in archaeal community composition were determined by sequencing of the archaeal 16S rRNA gene. Long-term thaw stimulated methanogenesis where methanogens initially dominated the archaeal community. Deposits of interstadial and interglacial (Eemian) origin, formed under higher temperatures and precipitation, displayed the greatest response to thaw. At the end of the incubations, a substantial shift in methanogenic community composition and a relative increase in hydrogenotrophic methanogens had occurred except for Eemian deposits in which a high abundance of potential acetoclastic methanogens were present. This study shows that only anaerobic CO2 production but not methane production correlates significantly with carbon and nitrogen content and that the methanogenic response to permafrost thaw is mainly constrained by the paleoenvironmental conditions during soil formation.

Developing a microbial ecological understanding of Arctic thermokarst lake sediments in a geochemical context is an essential first step toward comprehending the contributions of these systems to greenhouse gas emissions, and understanding how they may shift as a result of long term changes in climate. In light of this, we set out to study microbial diversity and structure in sediments from four shallow thermokarst lakes in the Arctic Coastal Plain of Alaska. Sediments from one of these lakes (Sukok) emit methane (CH4) of thermogenic origin, as expected for an area with natural gas reserves. However, sediments from a lake 10 km to the North West (Siqlukaq) produce CH4 of biogenic origin. Sukok and Siqlukaq were chosen among the four lakes surveyed to test the hypothesis that active CH4-producing organisms (methanogens) would reflect the distribution of CH4 gas levels in the sediments. We first examined the structure of the little known microbial community inhabiting the thaw bulb of arctic thermokarst lakes near Barrow, AK. Molecular approaches (PCR-DGGE and iTag sequencing) targeting the SSU rRNA gene and rRNA molecule were used to profile diversity, assemblage structure, and identify potentially active members of the microbial assemblages. Overall, the potentially active (rRNA dominant) fraction included taxa that have also been detected in other permafrost environments (e.g., Bacteroidetes, Actinobacteria, Nitrospirae, Chloroflexi, and others). In addition, Siqlukaq sediments were unique compared to the other sites, in that they harbored CH4-cycling organisms (i.e., methanogenic Archaea and methanotrophic Bacteria), as well as bacteria potentially involved in N cycling (e.g., Nitrospirae) whereas Sukok sediments were dominated by taxa typically involved in photosynthesis and biogeochemical sulfur (S) transformations. This study revealed a high degree of archaeal phylogenetic diversity in addition to CH4-producing archaea, which spanned nearly the phylogenetic extent of currently recognized Archaea phyla (e.g., Euryarchaeota, Bathyarchaeota, Thaumarchaeota, Woesearchaeota, Pacearchaeota, and others). Together these results shed light on expansive bacterial and archaeal diversity in Arctic thermokarst lakes and suggest important differences in biogeochemical potential in contrasting Arctic thermokarst lake sediment ecosystems.

The organic carbon of permafrost affected soils is receiving particular attention with respect to its fate and potential feedback to global warming. The structural and activity changes of methanogenic communities in the degrading permafrost-affected wetlands on the Tibetan Plateau can serve as fundamental elements for modelling feedback interaction of ecosystems to climate change. Hence, we aimed at anticipating if and how the rapid environmental changes occurring especially on the high altitude Tibetan platform will affect methanogenic communities. We identified methanogenic community composition, activity and abundance in wetland soils with different hydrological settings, permafrost extent and soil properties and pinpoint the environmental controls. We show that despite a pronounced natural gradient, the Tibetan high elevation wetland soils host a large methanogenic core microbiome. Hydrogenotrophic methanogens, in particular Methanoregula, and H2-dependent methanogenesis were overall dominant although acetoclastic methanogens in addition to hydrogenotrophs were among the dominating taxa in a minerotrophic fen. Tracing the Methanoregula community of the Tibetan Plateau using public databases revealed its global relevance in natural terrestrial habitats. Unlike the composition, the activity and abundance of methanogens varied strongly in the studied soils with higher values in alpine swamps than in alpine meadows. This study indicates that in the course of current wetland and permafrost degradation and the loss in soil moisture, a decrease in the methane production potential is expected on the high Tibetan Plateau but it will not lead to pronounced changes within the methanogenic community structure. (C) 2017 The Authors. Published by Elsevier Ltd.