黄顶菊入侵对土壤氨氧化古菌群落多样性的影响

为了明确入侵植物黄顶菊对土壤氮循环关键过程硝化作用的影响机制,本研究通过对其入侵地和未入侵地、根围土和根际土氨氧化古菌(ammonia-oxidizing archaea,AOA)的群落多样性分析,探讨了AOA对黄顶菊入侵的响应规律。结果表明:黄顶菊入侵增加了入侵地根围土AOA的多样性,AOA的Shannon指数表现为:入侵地根围土入侵地根际土未入侵地土壤,且差异显著。铵态氮含量与p H的变化都会影响土壤AOA的群落结构。系统发育树分析表明,土壤AOA主要隶属于氨氧化古菌的Nitrososphaera cluster。黄顶菊入侵导致的AOA的多样性水平的提升主要是由于入侵地氨氧化菌群种类增加所致。     

Stochasticity dominates assembly processes of soil nematode metacommunities on three Asian mountains

Nematodes play an important role in ecosystems; however, very little is known about their assembly processes and the factors influencing them. We studied nematode communities in bulk soils from three Asian mountain ecosystems to determine the assembly processes of free-living nematode metacommunities and their driving factors. On each mountain, elevations span a range of climatic conditions with the potential to reveal assembly processes that predominate across multiple biomes. A phylogenetic nu...     

长期施肥对水稻土剖面氨氧化古菌和细菌丰度及组成的影响

长期施肥影响稻田土壤理化性质和硝化微生物群落,但长期施肥对稻田不同土层氨氧化古菌(AOA)和氨氧化细菌(AOB)群落结构的影响尚不明确.以湖南宁乡稻田不同施肥制度长期定位试验为平台,选取不施肥(CK)、施秸秆有机肥(ST)、有机-无机肥配施(OM)和施全量化肥(NPK)4个处理,采用实时荧光定量PCR和Illumina...     

Determinants of the biodiversity patterns of ammonia-oxidizing archaea community in two contrasting forest stands

Purpose

The variation in soil microbial community patterns is primarily influenced by ecological processes associated with spatial distance and environmental heterogeneities. However, the relative importance of these processes in determining the patterns of soil microbial biodiversity in different successional forests remains unclear.

Materials and methods

Based on the species data from denaturing gradient gel electrophoresis (DGGE) analysis, we described the composition and beta diversity of ammonia-oxidizing archaea (AOA) community, an important functional microbial group in regulating nitrogen cycle, in a middle-succeed stand (60 years of secondary succession) and an undisturbed native stand in a subtropical forest in southern China. The composition pattern was examined using a multi-response permutation procedure (MRPP), and the beta diversity was described using the Sørensen index. The relative influence of edaphic, vegetational, spatial, and topographical factors on AOA composition and beta diversity was assessed by variation partitioning and multiple regression on distance matrices (MRM), respectively.

Results and discussion

We did not find any stand-specific patterns in AOA community composition in the two stands; however, the influential variables were different between the two stands; 7.3 and 4.5 % of the total variation in AOA community composition could be explained by edaphic (i.e., available potassium and total phosphorus) and spatial variables, respectively, in the middle-succeed stand, while 3.7 and 2.8 % of the variation were explained by spatial variable and available phosphorus, respectively, in the native stand. Soil total phosphorus influenced the beta diversity of AOA community most in the middle-succeed stand, while genetic distance of tree species was found to be the most important factor in driving the beta diversity pattern in the native stand.

Conclusions

Soil nutrients influenced the beta diversity of AOA community in the middle-succeed stand more than that in the native stand, while vegetation is more important in the native stand. The substantial unexplained variations were possibly due to the effects of other unmeasured variables. Nevertheless, dispersal process is more important in controlling AOA community composition in the native stand, while processes associated with environmental heterogeneities are more important in the middle-succeed stand in this subtropical forest.

     

Shrub-interspace dynamics alter relationships between microbial community composition and belowground ecosystem characteristics

In desert ecosystems, belowground characteristics are influenced chiefly by the formation and persistence of “shrub-islands of fertility” in contrast to barren plant interspaces. If soil microbial communities are exclusively compared between these two biogeochemically distinct soil types, the impact of characteristics altered by shrub species, especially soil C and N, are likely to be overemphasized and overshadow the role of other characteristics in structuring microbial composition. To determine how belowground characteristics influence microbial community composition, and if the relative importance of these characteristics shifts across the landscape (i.e., between and within shrub and interspace soils), changes in microbial communities across a 3000-year cold desert chronosequence were related to 27 belowground characteristics in surface and subsurface soils. When shrub and interspace communities in surface and subsurface soils were combined across the entire chronosequence, communities differed and were primarily influenced by soil C, NO₃⁻ concentrations, bulk density, pH, and root presence. Within shrub soils, microbial communities were shrub species-specific, especially in surface soils, highlighting differences in soil characteristics created by specific shrub species and/or similarity in stresses structuring shrub species and microbial communities alike. Microbial communities in shrub soils were not influenced by soil C, but by NO₃⁻ and NH₄⁺ concentrations, pH, and silt in surface soils; and Cl, P, soil N, and NO₃⁻ concentrations in subsurface soils. Interspace soil communities were distinct across the chronosequence at both depths and were strongly influenced by dune development. Interspace communities were primarily associated with soil stresses (i.e., high B and Cl concentrations), which decreased with dune development. The distribution of Gram-positive bacteria, Actinobacteria, and fungi highlighted community differences between and within shrub and interspace soils, while Gram-negative bacteria were common in all soils across the chronosequence. Of the 27 belowground characteristics investigated, 13 separated shrub from interspace communities, and of those, only five emerged as factors influencing community composition within shrub and interspace soils. As dunes develop across this cold desert chronosequence, microbial community composition was not regulated primarily by soil C, but by N and P availability and soil stresses in shrub soils, and exclusively by soil stresses in interspace soils.     

稻虾共作模式下稻田土壤氨氧化微生物丰度和群落结构的特征

【目的】研究稻虾共作模式下土壤氨氧化微生物数量、群落多样性及群落结构,深入了解该模式下的土壤微生态环境的演变。【方法】试验点在湖北省荆州市长江大学农学院基地,设置稻虾共作模式 (CR) 与常规中稻种植模式 (MR),借助荧光定量PCR技术与Illumina Miseq高通量测序平台,分析了土壤氨氧化细菌 (AOB) 与古菌 (AOA) 丰度、多样性及群落结构。【结果】与MR模式相比,CR模式显著提高了土壤硝态氮、总碳及总氮含量,对土壤pH、碱解氮及土壤碳氮比无显著影响。CR模式土壤AOA与AOB amoA基因拷贝数为3.13 × 105和7.01 × 105 copies/g干土,MR模式土壤AOA、AOB amoA基因拷贝数为1.41 × 105和3.87 × 105 copies/g干土,两个模式土壤AOB的数量均显著高于AOA,CR模式土壤AOA、AOB的数量均显著高于MR模式 (P < 0.05)。α群落多样性指数表明,相比MR,CR模式显著降低了土壤AOA群落多样性,对AOB群落多样性无显著影响。Venn结果分析,CR模式增加了AOA amoA基因的物种,改变了AOB amoA基因的物种组成,且AOB amoA物种数量下降。在属水平上,norank_c_environmental_samples_p_Thaumarchaeota、unclassified_k_norank_d_Archaea、norank_c_environmental_samples_p_Crenarchaeota、norank_p_environmental_samples_k_norank为AOA的优势类群,相对丰度占AOA amoA基因总序列的99.25%～99.46%,CR模式显著提高了norank_c_environmental_samples_p_Crenarchaeota在AOA群落属水平的相对丰度;unclassified_k_norank_d_Bacteria、norank_f_environmental_samples、norank_o_environmental_samples_c_Betaproteobacteria、unclassified_o_Nitrosomonadales为AOB的优势类群,相对丰度共占97.78%～98.49%,且CR模式显著增加了norank_o_environmental_samples_c_Betaproteobacteria与unclassified_o_Nitrosomonadales在AOB群落属水平的相对丰度。冗余分析 (RDA) 结果显示,土壤基本理化性质对于土壤AOA、AOB群落结构影响有着相似的趋势,其中对AOA、AOB群落结构影响最大的因子是硝态氮,其次分别为总碳、铵态氮、碱解氮、pH。根据RDA投影距离分析,稻虾共作模式对土壤AOA群落结构的影响大于AOB,且MR与稻虾共作模式土壤AOB的群落结构具有一定的相似度。【结论】稻虾共作模式显著降低了AOA群落多样性,而对AOB群落无显著影响;稻虾共作模式显著增加了AOA与AOB的丰度并显著影响了群落结构组成。土壤硝态氮、总碳、铵态氮、碱解氮、pH含量是导致土壤微生物数量、多样性及群落结构变化的主要原因。     

Community patterns of soil bacteria and nematodes in relation to geographic distance

Ecosystems consist of aboveground and belowground subsystems and the structure of their communities is known to change with distance. However, most of this knowledge originates from visible, aboveground components, whereas relatively little is known about how soil community structure varies with distance and if this variability depends on the group of organisms considered. In the present study, we analyzed 30 grasslands from three neighboring chalk hill ridges in southern UK to determine the effect of geographic distance (1–198 km) on the similarity of bacterial communities and of nematode communities in the soil. We found that for both groups, community similarity decayed with distance and that this spatial pattern was not related to changes either in plant community composition or soil chemistry. Site history may have contributed to the observed pattern in the case of nematodes, since the distance effect depended on the presence of different nematode taxa at one of the hill ridges. On the other hand, site-related differences in bacterial community composition alone could not explain the spatial turnover, suggesting that other factors, such as biotic gradients and local dispersal processes that we did not include in our analysis, may be involved in the observed pattern. We conclude that, independently of the variety of causal factors that may be involved, the decay in similarity with geographic distance is a characteristic feature of both communities of soil bacteria and nematodes.     

Bacterial community structure and function change in association with colonizer plants during early primary succession in a glacier forefield

Plants directly interact with the soil microbial community through litter inputs and root exudates, and these interactions may be particularly important in nutrient poor soils that typically characterize early ecosystem development. However, little is known regarding how plant–microbe interactions may actually drive ecosystem processes in early succession, a perspective this study helps to define. We investigated how soil microbial communities develop and interact with the establishment of the first plants in the recently exposed soils of the Mendenhall Glacier forefield near Juneau, AK, USA. We sampled soils from under two different plant species (alder, Alnus sinuata and spruce, Picea sitchensis) and from unvegetated areas; all samples were collected along a single soil transect that had been exposed for 6 years. The presence or absence of vegetation as well as the type of plant (i.e., alder vs. spruce) structured the soil microbial community. Furthermore, asymbiotic nitrogen (N) fixation rates, which were greater in vegetated soils, correlated with differences in bacterial community composition. Although soil microbial community composition varied with vegetation type, soil nutrient and carbon (C) pools did not correlate with bacterial community composition. Moreover, pH did not significantly vary by vegetation type, yet it was the only soil parameter that correlated with bacterial community composition. Vegetation type explained more of the variation in bacterial community composition than pH, suggesting that plant acidification of soils only partly explains the observed shifts in bacterial communities. Plant specific differences in bacterial community structure may also relate to the chemical composition of litter and root exudates. Our research reveals differences in the bacterial community composition of vegetated soils, and how such differences may promote shifts in fundamental biogeochemical processes, such as rates of asymbiotic N fixation, in early stages of primary succession where low N availability may limit bacterial and plant growth and thus constrain ecosystem development. As such, this suggests that plant–soil microbe interactions in themselves may drive processes that shape the trajectory of primary succession.     

Shift in abundance and structure of soil ammonia-oxidizing bacteria and archaea communities associated with four typical forest vegetations in subtropical region

Purpose

Nitrogen (N) is one of the most important elements that can limit plant growth in forest ecosystems. Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are considered as the key drivers of global N biogeochemical cycling. Soil ammonia-oxidizing microbial communities associated with subtropical vegetation remain poorly characterized. The aim of this study was to determine how AOA and AOB abundance and community structure shift in response to four typical forest vegetations in subtropical region.

Materials and methods

Broad-leaved forest (BF), Chinese fir forest (CF), Pinus massoniana forest (PF), and moso bamboo forest (MB) were widely distributed in the subtropical area of southern China and represented typical vegetation types. Four types of forest stands of more than 30 years grew adjacent to each other on the same soil type, slope, and elevation, were chosen for this experiment. The abundance and community structure of AOA and AOB were characterized by using real-time PCR and denaturing gradient gel electrophoresis (DGGE). The impact of soil properties on communities of AOA and AOB was tested by canonical correspondence analysis (CCA).

Results and discussion

The results indicated that AOB dominated in numbers over AOA in both BF and MB soils, while the AOA/AOB ratio shifted with different forest stands. The highest archaeal and bacterial amoA gene copy numbers were detected in CF and BF soils, respectively. The AOA abundance showed a negative correlation with soil pH and organic C but a positive correlation with NO₃ ^??N concentration. The structures of AOA communities changed with vegetation types, but vegetation types alone would not suffice for shaping AOB community structure among four forest soils. CCA results revealed that NO₃ ^??N concentration and soil pH were the most important environmental gradients on the distribution of AOA community except vegetation type, while NO₃ ^??N concentration, soil pH, and organic C significantly affected the distribution of the AOB communities.

Conclusions

These results revealed the differences in the abundance and structure of AOA and AOB community associated with different tree species, and AOA was more sensitive to vegetation and soil chemical properties than AOB. N bioavailability could be directly linked to AOA and AOB community, and these results are useful for management activities, including forest tree species selection in areas managed to minimize N export to aquatic systems.     

Abundance and community structure of ammonia-oxidizing archaea and bacteria in an acid paddy soil

Nitrification is essential to the nitrogen cycle in paddy soils. However, it is still not clear which group of ammonia-oxidizing microorganisms plays more important roles in nitrification in the paddy soils. The changes in the abundance and composition of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) were investigated by real-time PCR, terminal restriction fragment length polymorphism, and clone library approaches in an acid red paddy soil subjected to long-term fertilization treatments, including treatment without fertilizers (CT); chemical fertilizer nitrogen (N); N and potassium (NK); N and phosphorus (NP); N, P, and K (NPK); and NPK plus recycled crop residues (NPK+C). The AOA population size in NPK+C was higher than those in CT, while minor changes in AOB population sizes were detected among the treatments. There were also some changes in AOA community composition responding to different fertilization treatments. Still few differences were detected in AOB community composition among the treatments. Phylogenetic analysis showed that the AOA sequences fell into two main clusters: cluster A and cluster soil/sediment. The AOB composition in this paddy soil was dominated by Nitrosospira cluster 12. These results suggested that the AOA were more sensitive than AOB to different fertilization treatments in the acid red paddy soil.     

Phylogenetic structure of arbuscular mycorrhizal community shifts in response to increasing soil fertility

Understanding the underlying mechanisms driving responses of belowground communities to increasing soil fertility will facilitate predictions of ecosystem responses to anthropogenic eutrophication of terrestrial systems. We studied the impact of fertilization of an alpine meadow on arbuscular mycorrhizal (AM) fungi, a group of root-associated microorganisms that are important in maintaining sustainable ecosystems. Species and phylogenetic composition of AM fungal communities in soils were compared across a soil fertility gradient generated by 8 years of combined nitrogen and phosphorus fertilization. Phylogenetic patterns were used to infer the ecological processes structuring the fungal communities. We identified 37 AM fungal virtual taxa, mostly in the genus Glomus. High fertilizer treatments caused a dramatic loss of Glomus species, but a significant increase in genus richness and a shift towards dominance of the lineage of Diversispora. AM fungal communities were phylogenetically clustered in unfertilized soil, random in the low fertilizer treatment and over-dispersed in the high fertilizer treatments, suggesting that the primary ecological process structuring communities shifted from environmental filtering (selection by host plants and fungal niches) to a stochastic process and finally to competitive exclusion across the fertilization gradient. Our findings elucidate the community shifts associated with increased soil fertility, and suggest that high fertilizer inputs may change the dominant ecological processes responsible for the assembly of AM fungal communities towards increased competition as photosynthate from host plants becomes an increasingly limited resource.     

Succession of bacterial community and methanotrophy during lake shrinkage

Purpose

The shrinkage of vast inland lakes affects microbially mediated soil biogeochemical processes, which are critical for maintaining ecosystem sustainability, such as microbial diversity and a balanced CH₄ budget. Here we aimed to elucidate shifts in the bacterial community and methanotrophy during the shrinkage of a saline lake.

Materials and methods

Sediments and soils along a gradient transecting a saline lake, saline riparian land, and grassland were collected. The succession of microbial communities was characterized by high-throughput sequencing of the V4-V5 region of 16S rRNA genes coupled to non-metric multidimensional scaling (NMDS), linear discriminant effect size (LEfSe), community assembly, and co-occurrence network analyses. We further incubated these samples under a 10% CH₄ (v/v) atmospheric condition to determine the response of methane oxidation potentials and of methanotrophs to lake shrinkage by using pmoA-based qPCR and amplicon sequencing.

Results and discussion

LEfSe and NMDS analyses showed significant differences in bacterial communities among 3 stages of lake shrinkage. The microbial taxa with the highest increase were phylogenetically affiliated with unclassified Rhizobiales, Panacagrimonas, and Pseudomonas in saline and grassland soils when compared with sediments. Microbial community assembly was largely determined by deterministic rather than stochastic processes (NTI?>?2). The drastic increase of Methylocystis-like (type II) methanotrophs was observed during lake shrinkage, while type I methanotrophs showed a decreasing trend. However, upon consuming high-concentration methane of about 10%, type I methanotrophs dominated methane-oxidizing communities in lake sediment (Methylomonas), riparian saline soil (Methylomicrobium), and grassland soil (Methylobacter). Structural equation model identified soil pH, C/N ratio, and soil texture as key factors affecting methane oxidation rates and the methanotrophic community.

Conclusions

Lake shrinkage showed profound impacts on the overall bacterial communities and methane oxidizers. Soil physico-chemical properties likely shaped the bacterial community and phylogenetically distinct methanotrophs during lake shrinkage.

     

Direct and indirect influence of arbuscular mycorrhizal fungi on abundance and community structure of ammonia oxidizing bacteria and archaea in soil microcosms

Both arbuscular mycorrhizal (AM) fungi and ammonia oxidizers are important soil microbial groups in regulating soil N cycling. However, knowledge of their interactions, especially the direct influences of AM fungi on ammonia oxidizers is very limited to date. In the present study, a controlled microcosm experiment was established to examine the effects of AM fungi and N supply level on the abundance and community structure of ammonia oxidizing bacteria (AOB) and archaea (AOA) in the rhizosphere of alfalfa plants (Medicago sativa L.) inoculated with AM fungus Glomus intraradices. Effects were studied using combined approaches of quantitative polymerase chain reaction (qPCR) and terminal-restriction fragment length polymorphism (T-RFLP). The results showed that inoculation with AM fungi significantly increased the plant dry weights, total N and P uptake. Concomitantly, AM fungi significantly decreased the amoA gene copy numbers of AOA and AOB in the root compartment (RC) but not in the hyphal compartment (HC). Moreover, AM fungi induced some changes in AOA community structure in HC and RC, while only marginal variations in AOA composition were observed to respond to N supply level in HC. Neither RC nor HC showed significant differences in AOB composition irrespective of experimental treatments. The experimental results suggested that AM fungi could directly shape AOA composition, but more likely exerted indirect influences on AOA and AOB abundance via the plant pathway. In general, AM fungi may play an important role in mediating ammonia oxidizers, but the AOA community appeared to be more sensitive than the AOB community to AM fungi.     

pH-dependent distribution of soil ammonia oxidizers across a large geographical scale as revealed by high-throughput pyrosequencing

Purpose

Ammonia-oxidizing archaea (AOA) and bacteria (AOB) are ubiquitous and important for nitrogen transformations in terrestrial ecosystems. However, the distribution patterns of these microorganisms as affected by the terrestrial environments across a large geographical scale are not well understood. This study was designed to gain insights into the ecological characteristics of AOA and AOB in 65 soils, collected from a wide range of soil and ecosystem types.

Materials and methods

Barcoded pyrosequencing in combination with quantitative PCR was employed to characterize the relative abundance, diversity, and community composition of archaeal 16S rRNA gene, and AOA and AOB amoA genes in 65 soil samples.

Results and discussion

The operational taxonomic unit richness and Shannon diversity of Thaumarchaeota, AOA, and AOB were highly variable among different soils, but their variations were best explained by soil pH. Soil pH was strongly correlated with the overall community composition of ammonia oxidizers, as measured by the pairwise Bray–Curtis dissimilarity across all sites. These findings were further corroborated by the evident pH-dependent distribution patterns of four thaumarchaeal groups (I.1a-associated, I.1b, I.1c, and I.1c-associated) and four AOB clusters (2, 3a.1, 10, and 12). The ratios of AOA to AOB amoA gene copy numbers significantly decreased with increasing pH, suggesting a competitive advantage of AOA over AOB in acidic soils.

Conclusions

These results suggest that the distribution of ammonia oxidizers across large-scale biogeographical settings can be largely predicted along the soil pH gradient, thus providing important indications for the ecological characteristics of AOA and AOB in different soils.     

水旱轮作对土壤微生物群落构建过程的影响机制

为探究稻田生态系统微生物学机制,采集水旱轮作稻田土壤,并以相同土壤母质下长期淹水的藕田土壤以及旱作的果树土壤为对照,研究了稻田生态系统细菌群落结构以及基于零模型的群落构建机制。结果表明:旱作和水旱轮作两个生态系统,由于频繁耕作以及施肥管理等农业措施形成特定的生态位格局,确定性过程主导群落构建。旱作生态系统下确定性过程占78.6%,随机性过程占10.7%;相对于旱作,由于水旱轮作的淹水条件,土壤肥力积累,水体连通性较好等特性导致内部环境变化缓和,其随机性过程(39.3%)影响增加,确定性过程(50.0%)下降;同理,长期淹水的水生生态系统中随机性群落构建(50.0%)成为主导过程。群落构建影响细菌群落结构和功能,因此随机性生态过程的增强进一步增加了细菌多样性以及物种生态网络的交互度和稳定性,增强了微生物抵抗外部环境扰动的能力,该过程有助于维持农田生态系统功能的稳定性和可持续性。     

Changing soil characteristics alter the arbuscular mycorrhizal fungi communities of Arabica coffee (Coffea arabica) in Ethiopia across a management intensity gradient

Coffee is the most important tropical agricultural commodity worldwide, cultivated in more than 70 countries. Despite the plant's huge economic importance, there is very limited knowledge on the association of arbuscular mycorrhizal fungi (AMF) with coffee roots. We investigated the environmental drivers affecting the diversity and community composition of AMF on Arabica coffee in its Ethiopian center of origin. We used 454 amplicon pyrosequencing to describe AMF communities in the roots of Arabica coffee plants that were sampled along a large management intensity gradient, covering the major Ethiopian coffee production systems. We identified AMF genera that have not been reported before in Arabica coffee production regions elsewhere in the world and show that high soil phosphorus availability decreases AMF diversity and that soil pH, nitrogen and phosphorus availability strongly affect AMF community composition. At the scale of our study (max. 82 km distance between sampling points, and 770 m altitude difference), no effect was found of spatial location or altitude on AMF communities. This is the first study analyzing the drivers of naturally occurring AMF in the roots of a globally important tropical crop, providing preliminary data to improve coffee production in its native and introduced range, through targeted intervention in coffee AMF communities.     

Different roles of rhizosphere effect and long-term fertilization in the activity and community structure of ammonia oxidizers in a calcareous fluvo-aquic soil

Ammonia oxidation is a critical step in the soil nitrogen (N) cycle and can be affected by the application of mineral fertilizers or organic manure. However, little is known about the rhizosphere effect on the function and structure of ammonia-oxidizing bacterial (AOB) and archaeal (AOA) communities, the most important organisms responsible for ammonia oxidation in agricultural ecosystems. Here, the potential nitrification activity (PNA), population size and composition of AOB and AOA communities in both the rhizosphere and bulk soil from a long-term (31-year) fertilizer field experiment conducted during two seasons (wheat and maize) were investigated using the shaken slurry method, quantitative real-time polymerase chain reaction and denaturing gradient gel electrophoresis. N fertilization greatly enhanced PNA and AOB abundance, while manure application increased AOA abundance. The community structure of AOB exhibited more obvious shifts than that of AOA after long-term fertilization, resulting in more abundant AOB phylotypes similar to Nitrosospira clusters 3 and 4 in the N-fertilized treatments. Moreover, PNA was closely correlated with the abundance and community structure of AOB rather than that of AOA among soils during both seasons, indicating that AOB play an active role in ammonia oxidation. Conversely, the PNA and population sizes of AOB and AOA were typically higher in the rhizosphere than the bulk soil, implying a significant rhizosphere effect on ammonia oxidation. Cluster and redundancy analyses further showed that this rhizosphere effect played a more important role in shaping AOA community structure than long-term fertilization. Overall, the results indicate that AOB rather than AOA functionally dominate ammonia oxidation in the calcareous fluvo-aquic soil, and that rhizosphere effect and fertilization regime play different roles in the activity and community structures of AOB and AOA.     

亚硝化球菌属(Nitrososphaera)可能是酸性土壤硝化作用的重要驱动者

选择初始pH相近的两个酸性土壤(JX-3和JX-7)样品进行培养试验,探讨了氨氧化古菌(ammonia-oxidizing archaea,AOA)和氨氧化细菌(ammonia-oxidizing bacteria,AOB)在酸性土壤硝化过程中所发挥的作用。结果显示,经过50 d的培养,JX-7样品硝化速率显著高于JX-3,且明显降低土壤pH。培养后,两个土壤样品AOB丰度均增加,但样品间没有显著差异;JX-7土壤AOA丰度显著增加,而JX-3无显著变化。两个土壤样品AOA群落组成本身存在分异,但对于同一样品培养前后均无显著分异;AOB群落组成在两土壤间没有分异,但培养前后分别有分异。培养后,JX-7样品中AOA优势属Nitrososphaera和某些未知微生物的个别OTUs绝对丰度显著增加,而两样品AOB中Nitrosospira属的一些OTUs的绝对丰度均显著增加。因此,所研究的酸性土壤样品中AOA是硝化作用的主要贡献者,而且AOA主要通过提高Nitrososphaera属中个别OTUs的丰度,而不是整个群落来调控硝化作用。     

Bacterial pH-optima for growth track soil pH, but are higher than expected at low pH

One of the most influential factors determining the growth and composition of soil bacterial communities is pH. However, soil pH is often correlated with many other factors, including nutrient availability and plant community, and causality among factors is not easily determined. If soil pH is directly influencing the bacterial community, this must lead to a bacterial community growth optimised for the in situ pH. Using one set of Iberian soils (46 soils covering pH 4.2-7.3) and one set of UK grassland soils (16 soils covering pH 3.3-7.5) we measured the pH-optima for the growth of bacterial communities. Bacterial growth was estimated by the leucine incorporation method. The pH-optima for bacterial growth were positively correlated with soil pH, demonstrating its direct influence on the soil bacterial community. We found that the pH from a water extraction better matched the bacterial growth optimum compared with salt extractions of soil. Furthermore, we also showed a more subtle pattern between bacterial pH growth optima and soil pH. While closely matched at neutral pHs, pH-optima became higher than the in situ pH in more acid soils, resulting in a difference of about one pH-unit at the low-pH end. We propose that an explanation for the pattern is an interaction between increasing overall bacterial growth with higher pHs and the unimodal pH-response for growth of bacterial communities.     

Biochar addition affected the dynamics of ammonia oxidizers and nitrification in microcosms of a coastal alkaline soil

Biochar amendments have frequently been reported to alter microbial communities and biogeochemical processes in soils. However, the impact of biochar application on bacterial (AOB) and archaeal ammonia oxidizers (AOA) remains poorly understood. In this study, we investigated the responses of AOB and AOA to the application of biochar derived from cotton stalk at rates of 5, 10, and 20 % by weight to a coastal alkaline soil during a 12-week incubation. The results showed that the amoA gene of AOB consistently outnumbered that of AOA, whereas only the AOA amoA gene copy number was significantly correlated with the potential ammonia oxidation (PAO) rate (P?<?0.01). The significant decrease of PAO rates in biochar treatments occurred after incubation for 4–6 weeks, which were distinctly longer than that in the control (2 weeks). The PAO rates were significantly different among treatments during the first 4 weeks of incubation (P?<?0.05), with the highest usually in the 10 % treatment. Biochar application significantly increased the abundance of both nitrifiers in the 4 weeks of incubation (P?<?0.05). Biochar amendment also decreased AOA diversity, but increased AOB diversity, which resulted in different community structures of both nitrifiers (P?<?0.01), as shown by the differences between the 5 % biochar and the control treatments. We conclude that biochar application generally enhanced the abundance and altered the composition of ammonia oxidizers; the rate of biochar application also affected the rate and dynamics of nitrification, and the risk for increasing the alkalinity and N leaching of the studied soil was lower with a lower application rate.