Soil physicochemical and microbial drivers of temperature sensitivity of soil organic matter decomposition under boreal forests

Soil organic matter(SOM)in boreal forests is an important carbon sink.The aim of this study was to assess and to detect factors controlling the temperature sensitivity of SOM decomposition.Soils were collected from Scots pine,Norway spruce,silver birch,and mixed forests(O horizon)in northern Finland,and their basal respiration rates at five different temperatures(from 4 to 28℃)were measured.The Q_(10) values,showing the respiration rate changes with a 10℃ increase,were calculated using a Gaussian function and were based on temperature-dependent changes.Several soil physicochemical parameters were measured,and the functional diversity of the soil microbial communities was assessed using the MicroResp?method.The temperature sensitivity of SOM decomposition differed under the studied forest stands.Pine forests had the highest temperature sensitivity for SOM decomposition at the low temperature range(0–12℃).Within this temperature range,the Q_(10) values were positively correlated with the microbial functional diversity index(H'_(mic))and the soil C-to-P ratio.This suggested that the metabolic abilities of the soil microbial communities and the soil nutrient content were important controls of temperature sensitivity in taiga soils.     

Linking diagnostic features to soil microbial biomass and respiration in agricultural grassland soil: a large‐scale study in Ireland

The functional potential of soil ecosystems can be predicted from the activity and abundance of the microbial community in relation to key soil properties. When describing microbial community dynamics, soil physicochemical properties have traditionally been used. The extent of correlations between properties, however, differs between studies, especially across larger spatial scales. In this research we analysed soil microbial biomass and substrate‐induced respiration of 156 samples from Irish grasslands. In addition to the standard physicochemical, soil type and land management variables, soil diagnostic properties were included to identify if these important soil–landscape genesis classes affected microbial biomass and respiration dynamics in Irish soil. Apart from physicochemical properties, soil drainage class was identified as having an important effect on microbial properties. In particular, biomass‐specific basal (qCO₂) and substrate‐induced respiration (SIR:CFE) were explained best by the soil drainage. Poorly drained soil had smaller values of these respiration measures than well‐drained soil. We concluded that this resulted from different groups within the microbial community that could use readily available carbon sources, which suggests a change in microbial community dynamics associated with soil texture and periods of water stress. Overall, our results indicate that soil quality assessments should include both physicochemical properties and diagnostic classes, to provide a better understanding of the behaviour of soil microbial communities.

Highlights

• Assessing the effect of soil diagnostic features and properties on microbial biomass and respiration
• A soil biological survey from 156 grassland sites in Ireland
• Soil drainage class has an important effect on microbial properties
• Soil quality assessments should include both physicochemical properties and diagnostic classes

     

Tree species effects on soil enzyme activities through effects on soil physicochemical and microbial properties in a tropical montane forest on Mt. Kinabalu, Borneo

Tree species influence on the soil mineralization process can regulate overall nutrient cycling in a forest ecosystem, which may occur through their effects on substrate quality, soil physicochemical properties and soil microbial community. We investigated tree species effects on soil enzyme activities in a tropical montane forest on Mt. Kinabalu, Borneo. Specifically, we analyzed C- and P-degrading enzyme activities, as well as the relationships among the enzyme activities, soil physicochemical properties, substrate quality (C, N, and P concentrations), and microbial composition in the top 5 cm soils beneath conifers (Dacrycarpus imbricatus and Dacrydium gracilis) and broadleaves (Lithocarpus clementianus, Palaquium rioence, and Tristaniopsis clementis). Activities of acid phosphatase and β-d-glucosidase were significantly different among the tree species. Soil moisture, total C and N content and microbial lipid abundance (a proxy for microbial composition) could influence the enzyme activities although the relative contributions of microbial composition to the enzyme activities might be smaller. A higher acid phosphatase activity beneath Dacrydium than those beneath the other tree species can compensate for a lower concentration of P in available fractions beneath Dacrydium. This localized mineralization activity could subsequently influence soil nutrient availability in this forest.     

Long-term impact of fertilization on activity and composition of bacterial communities and metabolic guilds in agricultural soil

To explore long-term impact of organic and inorganic fertilizers on microbial communities, we targeted both the total bacterial community and the autotrophic ammonia oxidizing bacteria (AOB) in soil from six treatments at an experimental field site established in 1956: cattle manure, sewage sludge, Ca(NO₃)₂, (NH₄)₂SO₄, unfertilized and unfertilized without crops. All plots, except the bare fallows, were cropped with maize. Effects on activity were assessed by measuring the basal respiration and substrate induced respiration (SIR) rates, and the potential activity of the AOB. To determine the bacterial community composition, 16S rRNA genes were used to fingerprint total soil communities by terminal restriction fragment length polymorphism analysis and AOB communities by denaturing gradient gel electrophoresis. The fertilization regimes had clear effects on both activity and composition of the soil communities. Basal respiration and r, which was kinetically derived as the exponentially growing fraction of the SIR-response, correlated well with the soil organic C content (r=0.93 and 0.66, respectively). Soil pH ranged from 3.97 to 6.26 in the treatments and was found to be an important factor influencing all microbial activities. pH correlated negatively with the ratio between basal respiration and SIR (r=0.90), indicating a decreased efficiency of heterotrophic microorganisms to convert organic carbon into microbial biomass in the most acid soils with pH 3.97 and 4.68 ((NH₄)₂SO₄ and sewage sludge fertilized plots, respectively). The lowest SIR and ammonia oxidation rates were also found in these treatments. In addition, these treatments exhibited individually different community fingerprints, showing that pH affected the composition of AOB and total bacterial communities. The manure fertilized plots harbored the most diverse AOB community and the pattern was linked to a high potential ammonia oxidation activity. Thus, the AOB community composition appeared to be more strongly linked to the activity than the total bacterial communities were, likely explained by physiological differences in the populations present.     

Effects of straw and its biochar applications on the abundance and community structure of CO2-fixing bacteria in a sandy agricultural soil

Purpose

Crop straw and biochar application can potentially increase carbon sequestration and lead to changes in the microbial community in agricultural soils. Sequestration of CO₂ by autotrophic microorganisms is key to biogeochemical carbon cycling in soil ecosystems. The effects of straw and its biochar, derived from slow pyrolysis, on CO₂ fixation bacteria in sandy soils, remain unclear. Therefore, this study compared the response of abundance and community of CO₂ fixation bacteria to the two straw application methods in a sandy agricultural soil. The overall aim of the study was to achieve an efficient use of straw residues for the soil sustainablility.

Materials and methods

We investigated the soil organic carbon content and autotrophic bacteria over four consecutive years (2014–2018) in a field experiment, including the following four treatments: whole maize straw amendment (S), whole maize straw translated biochar amendment (B), half biochar and half straw amendment (BS), and control (CK) without straw or biochar amendment. The autotrophic bacterial abundance and community structure were measured using molecular methods of real-time PCR, terminal restriction fragment length polymorphisms (T-RFLP), and a clone library targeting the large subunit gene (cbbL) of ribulose-1,5-bisphosphate carboxylase/oxygenase.

Results and discussion

The results showed that the content of soil total organic carbon (TOC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC) in B, S, and BS treatments was significantly increased compared with the CK treatment. Soil TOC and available potassium (AK) in the B treatment significantly increased by 15.4% and 23.3%, respectively, but soil bulk density, DOC, and MBC significantly decreased by 8.5%, 10.6%, and 14.5%, respectively, compared with the S treatment. The abundance of the cbbL gene as well as of the bacterial 16S rRNA gene increased significantly in straw or biochar application treatments as compared to the CK treatment. The B treatment, but not the BS treatment, significantly increased the cbbL gene abundance when compared to the S treatment. No significant differences were observed in the bacterial 16S rRNA gene abundance among the three straw or biochar applications. The application of straw biochar could increase the diversity of the autotrophic bacteria, which also altered the overall microbial composition. Physicochemical properties of the soil, such as soil pH, SOC, and bulk density, can help explain the shift in soil microbial composition observed in the study.

Conclusions

Taken together, our results suggest that straw biochar, rather than straw application, leads to an increase in the abundance and diversity of CO₂-fixing bacteria, which would be advantageous for soil autotrophic CO₂ fixation.

     

城郊土壤不透水表面有土壤机碳转化及其相关性质的研究

Installation of impervious surface in urban area prevents the exchange of material and energy between soil and other environmental counterparts, thereby resulting in negative effects on soil function and urban environment. Soil samples were collected at 0-20 cm depth in Nanjing City, China, in which seven sites were selected for urban open soils, and fourteen sites with similar parent material were selected for the impervious-covered soils, to examine the effect of impervious surface on soil properties and microbial activities, and to determine the most important soil properties associated with soil organic carbon （SOC） transformation in the urban soils covered by impervious surfaces. Soil organic carbon and water-soluble organic carbon （WSOC） concentrations, potential carbon （C） and nitrogen （N） mineralization rates, basal respiration, and physicochemical properties with respect to C transformation were measured. Installation of impervious surface severely affected soil physicochemical properties and microbial activities, e.g., it significantly decreased total N contents, potential C mineralization and basal respiration rate （P 〈 0.01）, while increased pH, clay and Olsen-P concentrations. Soil organic carbon in the sealed soils at 0-20 cm was 2.35 kg m-2, which was significantly lower than the value of 4.52 kg m-2 in the open soils （P 〈 0.05）. Canonical correlation analysis showed WSOC played a major role in determining SOC transformation in the impervious-covered soil, and it was highly correlated with total N content and potential C mineralization rate. These findings demonstrate that installation of impervious surface in urban area, which will result in decreases of SOC and total N concentrations and soil microbial activities, has certain negative consequences for soil fertility and long-term storage of SOC.     

Localization of atmospheric H2-oxidizing soil hydrogenases in different particle fractions of soil

Low atmospheric H₂ concentrations (0.55 ppmv) are oxidized in soils by a high-affinity activity with typical characteristics of an abiontic soil enzyme. This activity was measured in a meadow cambisol and a forest cambisol. In both soils, the maximum activity was reached at a soil moisture of about 20% water-holding capacity, and was localized in the top A_h horizon. The soils were fractionated by dry sieving and wet filtration into nine different particle-size fractions, ranging from 3 to 2000 m in size. H₂ oxidation was measured by three different assays and was compared to the ATP content and microscopic counts of bacteria in the same fractions. In the meadow soil, the specific activities of H₂ oxidation increased with the particle size (maximum at 200–500 m), whereas ATP and bacterial counts showed no trend. In the forest soil, the specific activities of H₂ oxidation increased with the particle size up to 50–100 m, and then decreased again. ATP and bacterial counts, however, showed the opposite trend, i.e., decreased with an increasing particle size. Thus the H₂-oxidizing activity was not correlated with characteristic microbial biomass parameters. Although significant percentage (29–64%) of randomly isolated heterotrophic bacteria was able to oxidize H₂, this activity was too small to account for the H₂ oxidation in the soil. In both soils, most of the activity present was found in particles of 100–500 m in size. The recovery shifted to smaller size fractions when larger soil aggregates were broken up by wet instead of dry sieving. Attempts to extract the H₂-oxidizing activity from the soil particles were unsuccessful.     

Impacts of continuous excessive fertilization on soil potential nitrification activity and nitrifying microbial community dynamics in greenhouse system

Purpose

Sampling and analysis of greenhouse soils were conducted in Shouguang, China, to study continuous excessive fertilization effect on nitrifying microbial community dynamics in greenhouse environment.

Materials and methods

Potential nitrification activity (PNA), abundance, and structure of nitrifying microbial communities as well as the correlations with soil properties were investigated.

Results and discussion

Short-term excessive fertilization increased soil nutrient contents and the diversity of nitrifying microbial communities under greenhouse cultivation. However, the abundance and diversity of nitrifying communities decreased greatly due to the increase of soil acidity and salinity after 14 years of high fertilization in greenhouse. There was a significant positive correlation between soil PNA and the abundance of ammonia-oxidizing bacteria (AOB) but not that of ammonia-oxidizing archaea (AOA) in topsoil (0–20 cm) when pH ≥7. Soil PNA and AOB were strongly influenced by soil pH. The groups of Nitrososphaeraceae, Nitrosomonadaceae, and Nitrospiraceae were predominant in the AOA, AOB, and nitrite-oxidizing bacteria (NOB) communities, respectively. Nitrifying community structure was significantly correlated with soil electrical salinity (EC), organic carbon (OC), and nitrate nitrogen (NO₃ ^?–N) content by redundancy analysis (RDA).

Conclusions

Nitrification was predominated by AOB in greenhouse topsoil with high fertilizer loads. Soil salinity, OC, NO₃ ^?–N content, and pH affected by continuous excessive fertilization were the major edaphic factors in shaping nitrifying community structure in greenhouse soils.

     

不同施肥方式下土壤氨氧化细菌的群落特征

为了研究长期定位施肥对棕壤中氨氧化细菌（ammonia-oxidizing bacteria,AOB）种群结构多样性和垂直分布特征的影响,本研究采用化学分析、荧光定量PCR（qPCR）和变性梯度凝胶电泳（PCR-DGGE）技术,针对沈阳农业大学试验区不同施肥方式（不施肥、低量无机氮肥、高量无机氮肥、无机氮肥与有机肥配施）下不同土壤深度（0~20 cm、20~40 cm、40~60 cm）的土壤理化性质、AOB丰度及种群多样性进行分析,比较不同施肥方式对土壤AOB种群的影响。结果显示,与不施肥相比,施肥会降低土壤pH,增加土壤铵态氮（70.5%~939.21%）和硝态氮（253.20%~625.48%）含量。随土壤深度增加,土壤pH升高,铵态氮和硝态氮含量除低量无机氮肥处理外,多呈降低趋势。土壤增施氮肥可提高AOB丰度,降低总细菌丰度。其中,0~20 cm土层中AOB丰度较高,且高量无机氮肥处理的AOB数量最高,为9.65×10⁵拷贝数·g^-1（干土）。DGGE图谱分析显示,不同处理下,AOB群落结构多样性指数存在明显差异（P<0.05）,各多样性指数均在表层（0~20 cm）最高,增施氮肥则显著降低AOB的多样性。聚类分析表明,4个施肥处理中,高量无机氮肥处理聚为一类,其他处理则因土壤深度不同而异;3个土壤深度中,除不施肥处理外,所有施肥处理均表现为0~20 cm、20~40 cm土层发生聚类,40~60 cm则明显与其他两层分开。冗余梯度分析（RDA）显示,硝态氮（P=0.027）是造成影响AOB群落结构差异的主要原因。上述研究结果表明,长期定位施肥土壤AOB的数量和群落结构多样性受施肥方式显著影响,并表现出明显的垂直分布特征。与无机氮肥相比,有机无机配施处理有助于改善土壤pH,维持不同土壤深度下AOB群落结构多样性。     

Effects of regenerating vegetation on soil enzyme activity and microbial structure in reclaimed soils on a surface coal mine site

The aim of this study was to evaluate the influence of reclaimed scenarios on soil enzyme activities and microbial community in a reclaimed surface coal mine on the Northwest Loess Plateau of China. Soil samples were collected from a bare land (CK), and a plantation (PL) and four mixed forests (MF1-4). Soil physicochemical characteristics, four enzyme activities and microbial abundance and T-RFLP (terminal restriction fragment length polymorphism) profiles were measured. Effects of reclaimed scenarios on soil nutrients content, enzyme activities and microbial community were pronounced. Soil organic carbon could be well used to predict the major differences in enzyme activities, and microbial abundance and composition. Soil enzyme activities were more significantly correlated with fungal abundance than bacterial and archaeal ones. The higher soil nutrient content, enzyme activities, and microbial abundance and diversity were from mixed forests and the lowest ones were from CK, which suggested mixed forests would be feasible scenarios in semi-arid Loess Plateau. Soil bacteria, archaea and fungi evolved with reclaimed process, but the influences of reclaimed scenarios on each domain of microbial abundance, diversity and composition were different. These findings suggested that soil bacteria, archaea and fungi play different ecological roles during restoration process.     

Effects of the invader Solidago canadensis on soil properties

A perennial goldenrod weed, Solidago canadensis, is rapidly spreading in China and now poses a serious threat to native ecosystem structure and function. Little is known about the effects of S. canadensis invasion on rhizosphere physico-chemical properties and microbial communities. The objective of this study was to compare the soil physico-chemical properties and microbial communities of invaded (two ecotone sites and one monoculture site) and native plant rhizospheres in field areas of Zhejiang Province, Eastern China. Compared with those in the native site, soil total nitrogen, total phosphorus, NO₃-N, available phosphorus content, and aggregate stability consistently decreased with S. canadensis invasion, while soil organic carbon, NH₄-N content, pH, and bulk density in the invaded sites significantly increased. Soil microbial biomass (expressed by carbon, nitrogen, or phosphorus content), activity (basal respiration and substrate induced respiration), and functional diversity (calculated from the average well color development (AWCD) of 31 carbon sources in a BIOLOG Ecoplate) significantly increased with S. canadensis invasion. Microbial utilization of carbohydrate groups significantly increased in the invaded sites, while the utilization of carboxylic acids and amines/amides groups significantly decreased. Principal components analysis (PCA) of the AWCD data indicated that the heavily invaded site (monoculture) was clearly separated from the native site. Redundancy analysis (RDA) indicated that soil organic carbon, NH₄-N, NO₃-N, and pH significantly impacted the dynamics of microbial parameters across the invaded sites. These results suggested that several soil chemical properties (e.g., organic carbon, NH₄-N, and pH) and microbial parameters (e.g., microbial biomass, basal respiration, substrate induced respiration, and functional diversity) might be used as indicators of S. canadensis invasion density.     

Responses of soil nitrous oxide production and abundances and composition of associated microbial communities to nitrogen and water amendment

Soil moisture and nitrogen (N) are two important factors influencing N₂O emissions and the growth of microorganisms. Here, we carried out a microcosm experiment to evaluate effects of soil moisture level and N fertilizer type on N₂O emissions and abundances and composition of associated microbial communities in the two typical arable soils. The abundances and community composition of functional microbes involved in nitrification and denitrification were determined via quantitative PCR (qPCR) and terminal restriction length fragment polymorphism (T-RFLP), respectively. Results showed that N₂O production was higher at 90% water-filled pore (WFPS) than at 50% WFPS. The N₂O emissions in the two soils amended with ammonium were higher than those amended with nitrate, especially at relatively high moisture level. In both soils, increased soil moisture stimulated the growth of ammonia-oxidizing bacteria (AOB) and nitrite reducer (nirK). Ammonium fertilizer treatment increased the population size of AOB and nirK genes in the alluvial soil, while reduced the abundances of ammonia-oxidizing archaea (AOA) and denitrifiers (nirK and nosZ) in the red soil. Nitrate addition had a negative effect on AOA abundance in the red soil. Total N₂O emissions were positively correlated to AOB abundance, but not to other functional genes in the two soils. Changed soil moisture significantly affected AOA rather than AOB community composition in both soils. The way and extent of N fertilizers impacted on nitrifier and denitrifier community composition varied with N form and soil type. These results indicate that N₂O emissions and the succession of nitrifying and denitrifying communities are selectively affected by soil moisture and N fertilizer form in the two contrasting types of soil.     

Naphthalene addition to soil surfaces: A feasible method to reduce soil micro-arthropods with negligible direct effects on soil C dynamics

Soil fauna are a key component of soil biodiversity and a driver of soil functioning. While the importance of soil fauna is well recognized, quantitative estimates of the role of soil fauna on soil biogeochemical processes, such as plant litter decomposition, are limited by methodological constraints. The addition of naphthalene, a polycyclic aromatic hydrocarbon (C₁₀H₈), to suppress soil fauna has been used for decades in decomposition experiments, but its efficacy remains questioned. In fact, we lack a rigorous field assessment of the efficacy of naphthalene additions for soil fauna suppression and potential non-target effects on the soil microbial community and carbon cycling. We added naphthalene at a high rate (477 g m⁻²) monthly for 23 months on the bare soil surface of a tallgrass prairie. We determined the effect of such additions on the abundance of nematodes and micro-arthropods along the soil profile to a depth of 20 cm at 11, 16 and 23 months after initiating naphthalene application. We used the variation in the natural ¹³C abundance of the naphthalene (δ¹³C – 25.5‰) as compared to the native soil (δ¹³C ∼ −17‰) to quantify naphthalene contribution to soil CO₂ efflux and microbial biomarkers (PLFA). Naphthalene addition significantly reduced the abundance of oribatid mites (−45%), predatory mites (−52%) and springtails (−49%), but did not affect nematode abundance. The ¹³C abundance of a few Gram-negative (cy17:0, 18:1ω7c, 16:1ω7c), Gram-positive (a15:0, i15:0) and Actinobacteria (10Me-16:0, 10Me-18:0) PLFA markers decreased significantly in naphthalene treated plots, indicating bacterial utilization of naphthalene-derived C. Mixing models showed this contribution to be highly variable, with the highest naphthalene-C incorporation for Gram negative bacteria. Naphthalene-C was not incorporated in fungal PLFAs. This microbial utilization did not affect overall microbial abundance, community structure or activity, estimated as soil respiration. This experiment proves that naphthalene addition is a feasible method to reduce soil micro-arthropods in the field, with negligible direct effects on soil nematodes, microbial abundance and C dynamics.     

Changes in soil microbial community composition in response to fertilization of paddy soils in subtropical China

Repeated fertilizer applications to cultivated soils may alter the composition and activities of microbial communities in terrestrial agro-ecosystems. In this study, we investigated the effects of different long term fertilization practices (control (CK), three levels of mineral fertilizer (N₁P₁K₁, N₂P₂K₂, and N₃P₃K₃), and organic manure (OM)) on soil environmental variables and microbial communities by using phospholipid fatty acid (PLFA) biomarkers analysis in subtropical China. Study showed that OM treatment led to increases in soil organic carbon (SOC), total nitrogen (TN) and total phosphorus (TP) contents, while the mineral fertilizer treatment led to increases in dissolved organic carbon (DOC) content. Changes in soil microbial communities (eg. bacteria, actinomycetes) were more noticeable in soils subjected to organic manure applications than in the control soils or those treated with mineral fertilizer applications. Fungal PLFA biomarkers responded differently from the other PLFA groups, the numerical values of fungal PLFA biomarkers were similar for all the OM and mineral fertilizer treatments. PCA analysis showed that the relative abundance of most PLFA biomarkers increased in response to OM treatment, and that increased application rates of the mineral fertilizer changed the composition of one small fungal PLFA biomarker group (namely 18:3ω6c and 16:1ω5c). Further, from the range of soil environmental factors that we examined, SOC, TN and TP were the key determinants affecting soil microbial community. Our results suggest that organic manure should be recommended to improve soil microbial activity in subtropical agricultural ecosystems, while increasing mineral fertilizer applications alone will not increase microbial growth in paddy soils.     

棉秆生物质炭添加对棉田土壤理化性质及根际微生物群落结构的影响

以新疆滴灌棉田为研究对象,研究生物质炭施用对棉田土壤理化性质和棉花根际土壤微生物群落特征的影响。试验采集了不施生物质炭(CK)、施生物质炭3 t/hm²(BC1)、施生物质炭6 t/hm²(BC2)和施生物质炭9 t/hm²(BC3)4种处理棉花根际土壤,分析土壤理化性质和根际土壤微生物群落结构和组成的变化。结果表明,生物质炭施用后土壤pH和电导率分别下降了5.58% ~ 9.18%和5.38% ~ 18.04%;与CK相比,生物质炭施用使土壤有机质、全氮、全磷、碱解氮和有效磷含量均显著增加,且BC3增加效果最好,但生物质炭施用导致土壤钾含量显著降低。生物质炭施用显著降低了浮霉菌门(Planctomycetota)、芽单胞菌门(Gemmatimonadota)、厚壁菌门(Firmicutes)和被孢霉门(Mortierellomycota)相对丰度,但增加了子囊菌门(Ascomycota)、斯克尔曼氏菌属(Skermanella)、苔藓杆菌属(Bryobacter)、毛壳菌属(Chaetomium)、头束霉菌属(Cephalotrichum)、金孢属(Chrysosporium)和拟棘壳孢属(Pyrenochaetopsis)的相对丰度。另外,生物质炭施用降低了根际土壤微生物多样性和细菌丰富度,但根际土壤真菌的丰富度提高。生物质炭施用显著影响根际土壤微生物特别是真菌的群落结构,电导率、速效钾和pH是根际土壤微生物群落的主要影响因子。研究表明,生物质炭施用可以改善棉田土壤理化性质进而影响根际土壤微生物群落组成和结构,9 t/hm²为本试验的推荐施用量。     

Effect of agricultural land use change on community composition of bacteria and ammonia oxidizers

Purpose

Soil microbial communities can be strongly influenced by agricultural practices, but little is known about bacterial community successions as land use changes. The objective of this study was to determine microbial community shifts following major land use changes in order to improve our understanding of land use impacts on microbial community composition and functions.

Materials and methods

Four agricultural land use patterns were selected for the study, including old rice paddy fields (ORP), Magnolia nursery planting (MNP), short-term vegetable (STV), and long-term vegetable (LTV) cultivation. All four systems are located in the same region with same soil parent material (alluvium), and the MNP, STV, and LTV systems had been converted from ORP for 10, 3, and 30 years, respectively. Soil bacteria and ammonia oxidizer community compositions were analyzed by 454 pyrosequencing and terminal restriction fragment length polymorphism, respectively. Quantitative PCR was used to determine 16S rRNA and amoA gene copy numbers.

Results and discussion

The results showed that when land use was changed from rice paddy to upland systems, the relative abundance of Chloroflexi increased whereas Acidobacteria decreased significantly. While LTV induced significant shifts of bacterial composition, MNP had the highest relative abundance of genera GP1, GP2, and GP3, which were mainly related to the development of soil acidity. The community composition of ammonia-oxidizing bacteria (AOB) but not ammonia-oxidizing archaea was strongly impacted by the agricultural land use patterns, with LTV inducing the growth of a single super predominant AOB group. The land use changes also induced significant shifts in the abundance of 16S rRNA and bacterial amoA genes, but no significant differences in the abundance of archaea amoA was detected among the four land use patterns. Soil total phosphorous, available phosphorous, NO₃ ^?, and soil organic carbon contents and pH were the main determinants in driving the composition of both bacteria and AOB communities.

Conclusions

These results clearly show the significant impact of land use change on soil microbial community composition and abundance and this will have major implications on the microbial ecology and nutrient cycling in these systems, some of which is unknown. Further research should be directed to studying the impacts of these microbial community shifts on nutrient dynamics in these agroecosystems so that improved nutrient management systems can be developed.     

Co-localization of atmospheric H2 oxidation activity and high affinity H2-oxidizing bacteria in non-axenic soil and sterile soil amended with Streptomyces sp. PCB7

Two complementary experimental approaches were utilized to examine the extent to which free soil hydrogenases and H₂-oxidizing bacteria contribute to the soil uptake of atmospheric H₂. First, high affinity hydrogenase activity and H₂-oxidizing bacteria were fractionated in non-axenic soil and axenic soil colonized with the high affinity H₂-oxidizing bacterium Streptomyces sp. PCB7. Non-axenic soil was fractionated by buoyant density centrifugation. High affinity H₂ oxidation activity measured in individual fractions was proportional to the copy number of hhyL gene, specifying the large subunit of putative high affinity [NiFe]-hydrogenases. 2.5% of the hydrogenase activity was recovered in bacteria-free soil extract. Similarly, sequential centrifugation and wet filtrations of strain PCB7-colonized soil dispersed in solubilization buffer caused a loss of the activity, at a ratio proportional to the number of living cells removed. No abiontic hydrogenase activity was detected in bacteria-free fractions. The second experimental approach was designed to verify whether or not the [NiFe]-hydrogenase of strain PCB7 retains high affinity H₂ oxidation activity in soil, under the abiontic state. H₂ oxidation rates of crude enzyme extract of strain PCB7 measured under aerobic and anaerobic conditions were indistinguishable, indicating that the high affinity hydrogenase of strain PCB7 is oxygen-tolerant. The hydrogenase activity of sterile soil spiked with as much as 0.14 mg_(protein) g_(soil-dw)⁻¹ was equivalent to the H₂-oxidation activity of only 10⁶-10⁷ CFU of strain PCB7 g_(soil-dw)⁻¹. Taken together, our results indicate that high affinity hydrogenase activity is proportional to the abundance of H₂-oxidizing bacteria in soil and, that abiontic hydrogenases contribute only a few percent of the total high affinity H₂ oxidation activity detected in soil.     

Microbial activity and bacterial composition of H2-treated soils with net CO2 fixation

The effects of H₂ gas treatment of an agricultural soil cultivated previously with a mixture of clover (Trifolium pratense) and alfalfa (Medicago sativa) on CO₂ dynamics and microbial activity and composition were analyzed. The H₂ emission rate of 250 nmol H₂ g⁻¹ soil h⁻¹ was similar to the upper limit of estimated H₂ amounts emitted from N₂ fixing nodules into the surrounding soil ([Dong, Z., Layzell, D.B., 2001. H₂ oxidation, O₂ uptake and CO₂ fixation in hydrogen treated soil. Plant and Soil 229, 1-12.]). After 1 week of H₂ supply to soil samples simultaneously with H₂ uptake net CO₂ production declined continuously and this finally led to a net CO₂ fixation rate in the H₂-treated soil of 8 nmol CO₂ g⁻¹ soil h⁻¹. The time course of H₂ uptake and CO₂ fixation in the soils corresponded with an increase in microbial activity and biomass of the H₂-treated soil determined by microcalorimetric measurements, fluorescence in situ hybridization analysis (FISH) and DNA staining (DAPI). Shifts in the bacterial community structure caused by the supply of H₂ were recorded. While the H₂ treatment stimulated β-and γ-subclasses of Proteobacteria, it had no significant effect on α-Proteobacteria. In addition, FISH-detectable bacteria of the Cytophaga-Flavobacterium-Bacteroides phylum increased in numbers.     

Long-term fertilisation regimes affect the composition of the alkaline phosphomonoesterase encoding microbial community of a vertisol and its derivative soil fractions

Alkaline phosphomonoesterase (ALP) mainly originates from soil microbial secretion and plays a crucial role in the turnover of soil phosphorus (P). To examine the response of ALP-encoding microbial communities (analysed for the biomarker of the ALP gene, phoD) of soils and derivative soil fractions to different fertilisation regimes, soil samples were collected from a long-term experimental field (over 35 years). The different organic P (Po) pools of soil fractions and the ALP activity of soil were also determined. Compared with chemical-only fertilised soils, the ALP activity was 232–815% higher in organic-amended soils, and the highest enzyme activity was observed in the organic-only fertilised treatment. The abundance of the phoD gene harbouring in soil fractions, determined by quantitative PCR (qPCR), was affected by different fertilisations. The highest abundance of the phoD gene was generally detected in the 2–63-μm-sized fraction (silt), but most phoD-encoding microbial species were associated to the 0.1–2-μm-sized fraction (clay) in the chemical-only fertilised soil. The contents of labile Po (LPo), moderately labile Po (MLPo) and fulvic acid-associated Po (FAPo) were significantly correlated with the phoD gene abundance, whereas only LPo content was significantly correlated with the ALP activity. The dominant phoD-encoding phylas were Actinobacteria and Proteobacteria, according to a high-throughput sequencing. Bradyrhizobium, a N₂-fixer identified as a phoD-encoding genus, showed the highest abundance in fertilised soils. The abundance of Bradyrhizobium, Streptomyces, Modestobacter, Lysobacter, Frankia and Burkholderia increased with the organic-only amendment and was significantly correlated with the ALP activity. According to structure equation models (SEM), pH and LPo content significantly and directly affected the ALP activity; the soil organic C (C_org) content was related to composition and abundances of phoD-harbouring microbial communities; since both microbial properties were correlated to the ALP activity, the C_org content was indirectly related to the ALP activity. In conclusion, soil management practices can be used to optimise the contents of soil available P and the organic P with regulation of soil ALP activity and the community composition of corresponding microbes.     

Timber harvesting alters soil carbon mineralization and microbial community structure in coniferous forests

Timber harvesting influences both above and belowground ecosystem nutrient dynamics. Impact of timber harvesting on soil organic matter (SOM) mineralization and microbial community structure was evaluated in two coniferous forest species, ponderosa pine (Pinus ponderosa) and lodgepole pine (Pinus contorta). Management of ponderosa pine forests, particularly even-aged stand practices, increased the loss of CO₂-C and hence reduced SOM storage potential. Changes in soil microbial community structure were more pronounced in ponderosa pine uneven-aged and heavy harvest stands and in lodgepole pine even-aged stand as compared to their respective unmanaged stands. Harvesting of trees had a negative impact on SOM mineralization and soil microbial community structure in both coniferous forests, potentially reducing coniferous forest C storage potential.