NC | Structure and function of soil microbiome reveal N2O release from global wetlands

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编译：Lin Limin     校稿：朱琪

论文ID

原名：Structure and function of the soil microbiome underlying N₂O emissions from global wetlands

译名：The structure and function of soil microbial groups reveal global wetlandN₂O释放

第一/通讯作者：Mohammad Bahram

作者单位：

1 Institute of Ecology and Earth Sciences, University of Tartu

2 Department of Ecology, Swedish University of Agricultural Sciences

期刊：Nature communications

发表时间：2022

研究背景

N₂OTo be able to deplete the ozone layer is produced by microbial greenhouse gas,The wetland soil isN₂OThe biggest release source.但N₂ORelease the key microbial species and the process is not clear.The article suggests that in wetland soil dry and warmN₂OTo release a quantity to higher,This is associated with the function of the microbial community diversity.同时,The article proved that although the archaea abundance is far lower than the bacteria,But the nitration archaea is global wetland soilN₂ORelease the key factor;Continued global warming, and intensify environmental changes may promote nitrification activity of archaea,The wetland soil become much moreN₂O释放源.

Although the wetland soil（Including the gley soils and peat soil）仅占全球8%的地表,However the wetland soil organic carbon storage is one of the biggest system.Microbial degradation in the soilC和NCan lead to greenhouse gas（GHG）A large number of release,包括N₂O.N₂OIs a kind of potent greenhouse gas,The greenhouse effect than potentialCO₂高265倍,At the same time is also the most important ozone-depleting substances.A growing number of wetland soil of land use change,例如植树造林、Into farmland land,These changes require drainage,This is a long-term consequencesN₂O释放.In order to reduce the wetland soilN₂O释放,We need to understand shape nitrogen cycle andN₂OKinetics of microbial activity related biochemical path as well as the important environmental factor.

Microbial process,The traditional denitrifying、Nitrifying bacteria, denitrifying and alienation nitrate is converted to ammonia nitrogen,都会产生N₂O（Mainly in hypoxia condition）.And ammonia oxidation is the first step on the nitrification process,It is a good oxygen process,Mainly performed by three kinds of bacteria：The standard of ammonia oxidizing bacteria（AOB）、Ammonia oxidizing archaea（AOA）And ammonia oxidizing bacteria completely（Comammox Nitrospira）.AOANot only directly produceN₂O,Also can produce denitrification reaction substrate（亚硝氮）.But to promote the foregoing microbial reactions、N₂OGeneration and know little about the environmental conditions of the consumption process.In a lot of soil environment,In promoting denitrification andN₂ORelease the aspects,AOAMay play has not been proved important role.

By means of in situN₂O测量、The determination of the world645A structure with potential function of wetland soil microbial,The authors evaluated the archaea、Bacteria and fungi in the nitrogen cycle andN₂OThe potential role in the release.

Study sites and sampling

In this paper, the sampling time for2011年8月到2018年6Month during plant growth;Sampling site includes six continents29Other areas include three types of climate：A（Tropical rain）、C（温带）和D（北方）气候类型（基于Köppen分类）.Gas and soil samples from the public areas or with the local community and/All people or property agreement in advance to collect,根据法律规定,Samples by customs officials, especially with their respective countries for scientific purpose of the exemption is transported from the country of origin to the laboratory.In all areas of comprehensive environmental condition,我们建立了76A wetland soil sampling point,Including the different vegetation（苔藓、莎草、草地、草本植物、Trees and bare soil）And the land use type（Natural marsh、Swamps and forests;Agricultural land、Hay fields and pastures;Peat exploration area）（图1a）.Study level 4 land use intensity index is used to quantify the impact of land use change：0-No agricultural land（Natural marsh、Swamp or bog Lin）;1-Moderate grazing or cut the grass（Once a year or less）;2-Intensive grazing or cut the grass（More than once a year）;3-耕地（Direct fertilizer or fertilizer）.

At each sampling area,作者建立了1-4A sampling station（共196个）,相距15-500m,To maximize access to environmental changes.Each sampling station equipped with3-5An opaquePVC 65 LTruncated cone sampler,间距为1.5-5m,And an observation well（多孔、直径50mm、The parcel in the geotextilePP-HT管;长度为1m）.645A truncated cone sampler,The static chamber method,使用PVC环（直径0.5m,Installed in the soil0.1m深处）测量N₂O通量.Before the gas sampling,稳定3-12小时,To reduce the insert ring interference with flux influence.Place the chamber at the top of a set of ring filling water ring.在1Hours during the trial,每隔20Minutes from the gas chamber at the top of the space sampling to50mLGlass jar.在3天内,Each location at least three times the sampling.During the gas sampling,From the underground water level observation well recorded.在10厘米和20Cm depth measuring soil temperature.

After the gas sampling,从0-10cmIn the depth of the test chamber to collect150-200gThe soil samples,And shipped to Estonia tartu laboratory.After the sample homogeneous physical and chemical analysis and divided into sub samplesDNA提取.Used for chemical analysis of samples stored in4°C下,Microbial samples stored in-20°C下.DNAExtract the work finished by the university of tartu environmental microbiology laboratory.在运输过程中,Soil samples to maintain in the acquisition of environmental soil temperature.

结果与讨论

01

全球N₂OEmissions model

Research data show that more warm soil and drastic change of land use may strengthen wetland soilN₂O释放.N₂OThe temperature of the release and the warmest month exponential relationship.同时,N₂ORelease was associated with a significant land use type,Maximum value appeared in the bare soil,The minimum value in forest soil.纬度越高,N₂OThe lower the release.与N₂O释放相反,潜在的N₂Peak production in the temperate climate,Is negatively related to the intensity of land use.Were also found in the study of different ecosystemN₂ORelease the increase and the temperature rise associated.

图1. 全球N₂ORelease the hotspots and in different land use types of nitration archaea relationship

02

全球N₂OEmissions and microbial diversity and category of relationship

与N₂ORelease the close to the equator the increase corresponding to the（图 1b）,As latitude lower,The diversity of archaea increased significantly.相反,Mid-latitude of wetland soil bacterial diversity was the highest;And fungal diversity and latitude but no significant relationship between the average annual temperature of10-15℃The peak area.Climate and soil factors on wetland soil microbial（Including the archaea、细菌和真菌）The influence of the diversity was the most obvious.The diversity of archaea depends on the soilC/N比例;土壤pHIs the most important factors affecting bacteria;Relevance and fungal diversity and environmental factors the weakest.

基于16S和18S rRNAAmplification of microbial species found,Proteobacteria,Acidobacteriota,以及ChloroflexiIs the best microbial abundance category.However, these microbes andN₂OIs not significantly related to release,而AOA的相对丰度（属于Thaumarchaeota门）与N₂ORelease the related.Based on the macro genomic data,In all eukaryotic and prokaryotic organisms,Soil Crenarchaeotic Group (SCG)与N₂ORelease the relevant.另外,Based on reading long sequencing technology（PacBio）在>5Get a sampling site620ArchaeaOTUs发现,11个OTUs（包括5个属于Nitrososphaerales目,For ammonia oxidizing archaea）与N₂ORelease was a positive correlation between.其中,N₂OEmissions to the closest‘Candidatus Nitrosotenuis chungbukensis MY2’(r=0.488,p<0.001)和‘Candidatus Nitrosocosmicus oleophilus MY3’的OTUsThe most significant correlation.These two kinds of pure cultures of archaea also prove that produceN₂O.Ammonia oxidizing archaea without fertilization or low ammonia nitrogen environment plays an important role in the process of nitrification.

图2. SSU rRNAThe relative abundance of the genetic data

03

宏Genome analysis reveals the worldN₂O排放量

In order to study the causeN₂ORelease the function of the path,The article USES the metagenomic analysis of orthologous genes（OGs）集群.In all the potentialN₂ORelease the related genes mainly group of archaea,古菌amoA基因(ENOG411114F)的相对丰度与N₂ORelease the relevant（r=0.625, p<0.001;图3）.Article found good anaerobic ammonia oxidation path toThaumarchaeotaThe door of the four ancient bacteria genera：Nitrososphaera、Nitrosocosmicus、Nitrosotenuis以及Nitrosarchaeum.Soil nitrate nitrogen concentration and archaeaamoAGene abundance show strong correlation(r=0.551,p<0.001).Comparative genomics analysis found that relative to the bacteria,Enrichment of archaea in ammonia oxidation path more.总体而言,本研究发现ThaumarchaeotaThe global wetland soilN₂OThe release of the plays a key role of potential.然而涉及Thaumarchaeota古菌N₂OThe path and enzyme type has not been clear.

图3. The ancient bacteria and archaeaamoAGenes and global wetland soilN₂ORelease a strong positive correlation

04

Drive the worldN₂OEmissions of functional genes

This study adopts the quantitativeqPCRThe method of the main genes in the nitrogen cycle absolute quantitative.Archaea ammonia single oxygenase gene（archaeal amoA）And bacteria, ammonia single oxygenase gene（bacterial amoA）与N₂ORelease a strong positive correlation.在低纬度地区,Ammonia oxidizing archaea abundance relative to the denitrifying bacteria increase andN₂O释放增加（图1）相一致.古菌amoAThe absolute abundance than bacteriaamoA,In the importance of wetland soil system middle of nitrification bacteria.

令人意外的是,The other major genes involved in nitrogen cycle and cannot well explainN₂O释放.Comammox amoA基因与N₂ORelease the correlation of the weaker,这可能是由于ComammoxAble to adapt to the low ammonia nitrogen environment or because ofComammox Nitrospira产N₂OThe relatively small amount of.In addition of anaerobic ammonia oxidation bacteria（Anammox）And the nitrate nitrogen/Nitrate nitrogen related anaerobic methane oxidation bacteria（n-damo）的丰度与N₂OEmissions without correlation.nosZ基因（Coding nitrous oxide reductase）的丰度与N₂OEmissions were positively correlated.N₂OThe nitrification gene（nirK和nirS）与N₂OHas no impact on emissions or correlation between.nir基因与nosZ基因（编码N₂O还原为N₂的酶）A strong correlation between.这也解释了nirHigh abundance of genetic soilN₂ORelease less.然而N₂Production andnosZAbundance and no significant correlation between.此外,Denitrification genes due to the large difference of different species,Not all of denitrifying bacteria and coding all this a series of gene.土壤pHAnd organic compound concentration may also affect denitrification produceN₂O.然而,Denitrifying bacteria than those who are richer nitrifying bacteria metabolism,Can make use of different compounds as energy and respiration,Reflect on their weaker environment correlation.

接下来,作者将N₂ORelease with the main gene involved in the nitrogen cycle of（基于qPCRGenetic absolute quantitative）The diversity of the relate,发现N₂OThe increase of the release is associated with an increased diversity of functional genes involved in nitrogen cycling（图4c）.This phenomenon may be due to the complementary between nitrogen related process,Especially denitrification and denitrifying process can produceN₂O.The complementary occurred in the dry wetland soil,This type of wetland soil will experience different oxygen anaerobic-aerobic conditions,Denitrifying microorganism of nitrate nitrogen can, as the substrate of denitrifying process.The change of environment conditions depends on the water level dynamic change,Changeful environment determines the biodiversity,Further influence the wetland soilN₂O排放.然而,The authors found that the soil factor（C/N比和pH）And the temperature on the degree of influence function genetic diversity is higher than the soil water content.In the research of functional genes,古菌amoAThe abundance and the temperature andC/NThan most relevant,Nitrogen cycle a similar genetic diversity.Didn't agree with the author expected is that,The species diversity of microorganisms andN₂OIs not significant correlation between the release of the,This is inconsistent with previous research.Species diversity and functional diversity of different results may be due to the activity of microbial species in the nitrogen cycle of functional redundancy.

图4. Nitrogen cycle gene as a main factor to explain the wetland soilN₂O释放

05

N₂ORelated environmental determinants of microbial community

The article further analysis to promote driveN₂ORelease of microbial species and the gene of environmental factor.古菌amoAAnd in the temperature show unimodal curve relationship,峰值出现在20℃(r²_adj=0.255,p<0.001).This study found before andAOAActive in the season of higher temperatures increase the laws.AOA/AOBThe ratio of a strong positive correlation,Means that the average annual temperature and soil temperature is strong positive correlation between,This also with relatively high temperature is beneficial toAOAThe situation of.The results show that soil temperature on the high side（>15℃）Combined with the suitable soil moisture may by promotingAOAThe increase of abundance exacerbatingN₂O释放.然而,Still need to verify the situation how toAOA与AOBThe relative balance between the compensation.

结论

In this paper, the analysis found the worldN₂OEmissions depends on the structure and function of wetland soil microbial groups and climate.Considering the coupling influence soil moisture and temperature,Archaea for the contribution of the dry wetland soil nitrogen cycle is important.此外,Archaea is ammonia oxidation path related to the abundance of important factor to reveal the global wetlandN₂O释放.This article complements previous studies（Archaea is mountain soil and seaN₂ORelease of the main contributors to）.全球AOAAnd they will be able to adapt to the distribution of low oxygen、Low concentration of ammonia nitrogen is probably they will be able to in the wetland soil nitrogen cycle microbiota plays a key role in.

总而言之,This article found nitrifying microorganisms toN₂ORelease the contribution of the higher than previously thought,同时,Nitrogen cycle related microbial diversity can be aN₂ORelease the predictor of comprehensive.In order to clarify the worldN₂OThe mechanism of release,We need to understand the different habitat types of nitrification and denitrification process and climate、植被、And the influence of land use.The authors forecast the future wetland soil drainage and the climate warming through adding archaea nitrification denitrification increases the substrate to promoteN₂O释放,To adjust the function of ecological system of wetland system to form negative impact.

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