Microbial PLFAs Research Articles

Photosynthetic carbon allocation in native and invasive salt marshes undergoing hydrological change

Biogeochemical processes mediated by plants and soil in coastal marshes are vulnerable to environmental changes and biological invasion. In particular, tidal inundation and salinity stress will intensify under future rising sea level scenarios. In this study, the interactive effects of flooding regimes (non-waterlogging vs. waterlogging) and salinity (0, 5, 15, and 30 parts per thousand (ppt)) on photosynthetic carbon allocation in plant, rhizodeposition, and microbial communities in native (Phragmites australis) and invasive (Spartina alterniflora) marshes were investigated using mesocosm experiments and 13CO2 pulse-labeling techniques. The results showed that waterlogging and elevated salinity treatments decreased specific root allocation (SRA) of 13C, rhizodeposition allocation (RA) 13C, soil 13C content, grouped microbial PLFAs, and the fungal 13C proportion relative to total PLFAs-13C. The lowest SRA, RA, and fungal 13C proportion occurred under the combined waterlogging and high (30 ppt) salinity treatments. Relative to S. alterniflora, P. australis displayed greater sensitivity to hydrological changes, with a greater reduction in rhizodeposition, soil 13C content, and fungal PLFAs. S. alterniflora showed an earlier peak SRA but a lower root/shoot 13C ratio than P. australis. This suggests that S. alterniflora may transfer more photosynthetic carbon to the shoot and rhizosphere to facilitate invasion under stress. Waterlogging and high salinity treatments shifted C allocation towards bacteria over fungi for both plant species, with a higher allocation shift in S. alterniflora soil, revealing the species-specific microbial response to hydrological stresses. Potential shifts towards less efficient bacterial pathways might result in accelerated carbon loss. Over the study period, salinity was the primary driver for both species, explaining 33.2–50.8 % of 13C allocation in the plant-soil-microbe system. We propose that future carbon dynamics in coastal salt marshes under sea-level rise conditions depend on species-specific adaptive strategies and carbon allocation patterns of native and invasive plant-soil systems.

Response of Organic Carbon Mineralization to Nitrogen Addition in Micro-aerobic and Anaerobic Layers of Paddy Soil

In field conditions, a micro-aerobic layer with 1 cm thickness exists on the surface layer of paddy soil owing to the diffusion of dissolved oxygen via flooding water. However, the particularity of carbon and nitrogen transformation in this specific soil layer is not clear. A typical subtropical paddy soil was collected and incubated with13C-labelled rice straw for 100 days. The responses of exogenous fresh organic carbon(13C-rice straw) and original soil organic carbon mineralization to nitrogen fertilizer addition[(NH4)2SO4]in the micro-aerobic layer(0-1 cm) and anaerobic layer(1-5 cm) of paddy soil and their microbial processes were analyzed based on the analysis of 13C incorporation into phospholipid fatty acid(13C-PLFAs). Nitrogen addition promoted the total CO2 and 13C-CO2 emission from paddy soil by 11.4% and 12.3%, respectively. At the end of incubation, with the addition of nitrogen, the total soil organic carbon (SOC) and13C-recovery rate from rice straw in the anaerobic layer were 2.4% and 9.2% lower than those in the corresponding micro-aerobic layer, respectively. At the early stage(5 days), nitrogen addition increased the total microbial PLFAs in the anaerobic layer with a consistent response of bacterial and fungal PLFAs. However, there was no significant effect from nitrogen on microbial abundance in the micro-aerobic layer. Nitrogen addition had no significant impact on the abundance of total 13C-PLFAs in the micro-aerobic and anaerobic layers, but the abundance of 13C-PLFAs for bacteria and fungi in the micro-aerobic layer was decreased dramatically. At the late stage(100 days), the effect of nitrogen addition on microbial PLFAs was consistent with that at the early stage. The abundances of total, bacterial, and fungal 13C-PLFAs were remarkably increased in the anaerobic layer. However, the abundance of 13C-PLFAs in the micro-aerobic layer showed no significant response to nitrogen addition. During the incubation, the content of NH4+-N in the anaerobic soil layer was higher than that in the micro-aerobic soil layer. This indicates that nitrogen addition increased microbial activity in the anaerobic soil layer caused by the higher NH4+-N concentration, as majority of microorganisms preferred to use NH4+-N. Consequently, the microbial utilization and decomposition of organic carbon in the anaerobic soil layer were accelerated. By contrast, richer available N existed in the form of NO3--N in the micro-aerobic soil layer owing to the ammoxidation process. Thus, the shortage of NO3--N preference microorganisms in the paddy soil environment prohibited the microbial metabolism of organic carbon in the micro-aerobic layer. As a whole, nitrogen fertilization enhanced organic carbon loss via microbial mineralization in paddy soil with a weaker effect in the micro-aerobic layer than that in the anaerobic layer, indicating the limited microbial metabolic activity in the surface micro-aerobic layer could protect the organic carbon stabilization in paddy soil. This study emphasizes the heterogeneity of paddy soil and its significant particularity of carbon and nitrogen transformation in micro-aerobic layers. Consequently, this study has implications for optimizing the forms and method for the application of nitrogen fertilizer in paddy cropping systems.

Soil phosphorus availability alters the correlations between root phosphorus-uptake rates and net photosynthesis of dominant C3 and C4 species in a typical temperate grassland of Northern China.

Phosphorus (P) fertilization can alleviate a soil P deficiency in grassland ecosystems. Understanding plant functional traits that enhance P uptake can improve grassland management. We measured impacts of P addition on soil chemical and microbial properties, net photosynthetic rate (Pn ) and nonstructural carbohydrate concentrations ([NSC]), and root P-uptake rate (PUR), morphology, anatomy, and exudation of two dominant grass species: Leymus chinensis (C3 ) and Cleistogenes squarrosa (C4 ). For L. chinensis, PUR and Pn showed a nonlinear correlation. Growing more adventitious roots compensated for the decrease in P transport per unit root length, so that it maintained a high PUR. For C. squarrosa, PUR and Pn presented a linear correlation. Increased Pn was associated with modifications in root morphology, which further enhanced its PUR and a greater surplus of photosynthate and significantly stimulated root exudation (proxied by leaf [Mn]), which had a greater impact on rhizosheath micro-environment and microbial PLFAs. Our results present correlations between the PUR and the Pn of L. chinensis and C. squarrosa and reveal that NSC appeared to drive the modifications of root morphology and exudation; they provide more objective basis for more efficient P-input in grasslands to address the urgent problem of P deficiency.

Life at the extreme: Plant-driven hotspots of soil nutrient cycling in the hyper-arid core of the Atacama Desert

The hyperarid core of the Atacama Desert represents one of the most intense environments on Earth, often being used as an analog for Mars regolith. The area is characterized by extremes in climate (e.g., temperature, humidity, UV irradiation) and edaphic factors (e.g., hyper-salinity, high pH, compaction, high perchlorates, and low moisture, phosphorus and organic matter). However, the halophytic C4 plant Distichlis spicata appears to be one of the few species on the planet that can thrive in this environment. Within this habitat it captures windblown sand leading to the formation of unique structures and the generation of above-ground phyllosphere soil. Using a combination of approaches (e.g., X-ray Computed Tomography, TXRF, δ13C/δ15N isotope profiling, microbial PLFAs, 14C turnover, phosphate sorption isotherms) we examined the factors regulating the biogeochemical cycling of nitrogen (N), phosphorus (P) and carbon (C) in both vegetated and unvegetated areas. Our results showed that D. spicata rhizomes with large aerenchyma were able to break through the highly cemented topsoil layer leading to root proliferation in the underlying soil. The presence of roots increased soil water content, P availability and induced a change in microbial community structure and promoted microbial growth and activity. In contrast, soil in the phyllosphere exhibited almost no biological activity. Organic C stocks and recent C4 plant derived input increased as follows: phyllosphere (1941 g C m−2; 85% recent) > soils under plants (575–748 g C m−2; 55–60%) > bare soils (491–642 g C m−2; 9–17%). Due to the high levels of nitrate in soil (>2 t ha−1) and high rates of P sorption/precipitation, our data suggest that the microbial activity is both C and P, but not N limited. Root-mediated salt uptake combined with foliar excretion and dispersal of NaCl into the surrounding area indicated that D. spicata was responsible for actively removing ca. 55% of the salt from the rhizosphere. We also demonstrate that NH3 emissions may represent a major N loss pathway from these soil ecosystems during the processing of organic N. We attribute this to NH3 volatilization to the high pH of the soil and slow rates of nitrification. In conclusion, we demonstrate that the extremophile D. spicata physically, chemically and biologically reengineers the soil to create a highly bioactive hotspot within the climate-extreme of the Atacama Desert.

Soil microbial community composition along chronosequence of the introduction of Phragmites australis at Suncheon Bay

Vegetations of coastal wetlands play a vital role in providing numerous ecological services to the coastal ecosystem and are also key factors affecting the biogeochemical processes in the soil. The acreage of Phragmites australis is expanding and gradually replacing the Suaeda japonica at Suncheon Bay, Republic of Korea. However, the changes in soil microbial community composition caused by Phragmites introduction is poorly characterized. In the present study, soil cores were collected to a depth of 1m (divided into 10 segments of 10 cm) from Suaeda-vegetated, the boundary of Suaeda- and Phragmites-vegetated, Phragmites-vegetated marshes (after 5 and 10 years of the introduction). These samples were analyzed for physico-chemical characteristics, enzyme activities, soil microbial community (phospholipid fatty acids profiling) and abundance of functional genes related to the methane cycle (mcrA, pmoA and dsrA). Results showed that introduction the of Phragmites increased the water content, pH and dissolved organic carbon content in the soil. The contents of total PLFA and microbial group biomarkers of PLFA were observed to be higher in the surface soil and decreased with soil depth. Early introduction of Phragmites (10 yr) sediments had the significantly highest concentrations of total as well as other microbial biomarkers PLFAs compared with other salt marshes. The relative abundance of biomarker PLFAs of Gram-negative bacteria was significantly higher in Phragmites compared to other salt marshes. The abundance of mcrA was significantly highest in Phragmites salt marshes (10 yr) and mixed salt marshes while the abundance of mcrA, pmoA and dsrA were lowest in Suaeda marshes. Our results reflect the chronological effects of the introduction of Phragmites on the physicochemical and microbial community composition which contribute to establishing the relationship between the plant introduction and soil biogeochemical processes in coastal salt marshes.

Response of Soil Organic Carbon Stock to Bryophyte Removal Is Regulated by Forest Types in Southwest China

Bryophytes play an important role in biogeochemical cycles and functions in forest ecosystems. Global climate changes have led to the population decline of bryophytes; however, the effects of bryophyte loss on the soil organic carbon stock and microbial dynamic remain poorly understood. Here, bryophytes were artificially removed to simulate the loss of bryophytes in two forests in Southwest China, i.e., evergreen broad-leaved forest and temperate coniferous forest. Soil physicochemical properties, microorganisms, and soil organic carbon stocks were analyzed and factors regulating soil organic carbon stocks were explored. Results showed that bryophyte removal significantly decreased soil organic carbon in the coniferous forest but had a negligible effect on the evergreen broad-leaved forest. Bryophyte removal had an insignificant effect on soil properties and microbial PLFAs except that soil nitrogen significantly increased in the 0–10 cm layer in the evergreen broad-leaved forest, while soil temperature and bulk density increased in the coniferous forest in the 0–10 and 10–20 soil layers, respectively. Soil organic carbon stocks increased by 14.06% in the evergreen forest and decreased by 14.39% in the coniferous forest. In the evergreen forest, most soil properties and microorganisms contributed to the change of soil organic carbon stocks, however, only soil organic carbon and depth had significant effects in the coniferous forest. Our findings suggest that soil physiochemical properties and microorganisms regulated the different responses of soil organic carbon stocks after bryophyte removal in the two forests. More research is needed to better understand the effects of understory plants on soil organic carbon stocks in various forest ecosystems.

Nitrogen deposition in low-phosphorus tropical forests benefits soil C sequestration but not stabilization

The stability of soil organic carbon (SOC) plays a vital role in C sequestration, and largely depends on the availability of soil nitrogen (N) and phosphorus (P). Understanding how different fractions of SOC respond to N and P availability and the underlying microbial mechanism is crucial for mitigating climate changes. Here, we assessed how soil N and P availability modifies different SOC fractions and the soil microbial communities in a tropical forest. We measured soil chemical properties, SOC fractions, microbial PLFA abundance, fungal rDNA and its predicted gene abundance, and extracellular enzyme activities within a field N and P addition experiment. P addition decreased the concentration of recalcitrant SOC and greatly increased the soil oxidative extracellular enzyme activities, while N addition increased active SOC, mainly light fractions, and decreased soil phenol oxidase activity. P addition also induced the greatest abundance of oxidoreductases. Additionally, the transferases, lyases, hydrolases, isomerases, and ligases were also expressed at higher levels after P addition. The results indicate that enhanced soil microbial activities after P addition accelerated recalcitrant SOC decomposition by higher oxidative enzyme activities. Given the increasing N deposition, tropical forests that characterized by a low P have a great potential to sequester more SOC which will mitigate climate change. However, the increase in SOC might be vulnerable to disturbance, because most of the increased C is the active SOC.

Co-analysis of cucumber rhizosphere metabolites and microbial PLFAs under excessive fertilization in solar greenhouse.

Fertilizer application is the most common measure in agricultural production, which can promote the productivity of crops such as cucumbers, but the problem of excessive fertilization occurs frequently in solar greenhouses. However, the effects of fertilization levels on cucumber rhizosphere soil microbes and metabolites and their relationships are still unclear. In order to determine how fertilization levels affect the rhizosphere microenvironment, we set up four treatments in the solar greenhouse: no-fertilization (N0P0K0), normal fertilization (N1P1K1), slight excessive fertilization (N2P2K2), and extreme excessive fertilization (N3P3K3). The results showed that fertilization treatments significantly increased cucumber yield compared to no-fertilization, but, the yield of N3P3K3 was significantly lower than that of N1P1K1 and N2P2K2. Fertilization levels had significant effects on rhizosphere microorganisms, and pH, NH4+-N and AP were the main environmental factors that affected the changes in microbial communities. The total PLFAs, the percentages of fungi and arbuscular mycorrhizal fungi (AMF) were significantly reduced and bacteria percentage was significantly increased in N3P3K3 compared to other fertilization treatments. Differential metabolites under different fertilization levels were mainly organic acids, esters and sugars. Soil phenols with autotoxic effect under fertilization treatments were higher than that of N0P0K0. In addition, compared with soil organic acids and alkanes of N0P0K0, N2P2K2 was significantly increased, and N3P3K3 was not significantly different. This suggested that cucumber could maintain microbial communities by secreting beneficial metabolites under slight excessive fertilization (N2P2K2). But under extremely excessive fertilization (N3P3K3), the self-regulating ability of cucumber plants and rhizosphere soil was insufficient to cope with high salt stress. Furthermore, co-occurrence network showed that 16:1ω5c (AMF) was positively correlated with 2-palmitoylglycerol, hentriacontane, 11-octadecenoic acid, decane,4-methyl- and d-trehalose, and negatively correlated with 9-octadecenoic acid at different fertilization levels. This indicated that the beneficial microorganisms in the cucumber rhizosphere soil promoted with beneficial metabolites and antagonized with harmful metabolites. But with the deepening of overfertilization, the content of beneficial microorganisms and metabolites decreased. The study provided new insights into the interaction of plant rhizosphere soil metabolites and soil microbiomes under the different fertilization levels.

Responses of soil microbial community structure to litter inputs.

Litter decomposition is one of the most important ecosystem processes, which plays a critical role in regu-lating nutrient cycling and energy flow in terrestrial ecosystems. The influence of litter inputs on soil microbial community is helpful for understanding the relationship between soil microbial diversity and terrestrial ecosystem function. We conducted a meta-analysis to examine how litter inputs affect soil microbial activity (fungi, bacteria, actinomycetes) and microbial biomass carbon, nitrogen in China. The results showed that compared with non-litter input, soil microbial biomass carbon and nitrogen were significantly increased by 3.9% and 4.4% respectively after litter inputs. Soil fungal PLFA, bacterial PLFA, and total microbial PLFA were increased by 4.0%, 3.1% and 2.4%, respectively. The effects of litter inputs differed significantly with climatic region, annual precipitation, vege-tation type, and soil pH. Under different climate conditions, the responses of soil microbe showed the trend of subtropical monsoon climatic region > temperate monsoon climatic region > temperate continental climatic region, which increased first and then decreased with increasing annual precipitation. Under different vegetation types, the responses of soil microbes showed the trend of broad-leaved forest > grassland ≈ mixed forest > coniferous forest.

Carbon Addition Modified the Response of Heterotrophic Respiration to Soil Sieving in Ectomycorrhizal-Dominated Forests

Soil heterotrophic respiration (Rh) is an important pathway of carbon (C) dioxide release from terrestrial soils to the atmosphere. It is often measured using sieved soil in a laboratory, but the uncertainty of how it is influenced by soil sieving persists, which limits the accuracy of predicting soil organic C dynamics in C models. To address how soil sieving during laboratory incubation affects Rh and its response to increased carbon availability, we investigated Rh in sieved and intact soil cores and its response to 13C-glucose addition. This was conducted through a 27-day laboratory incubation in four forests, including two ectomycorrhizal-dominated (ECM) forests and two arbuscular mycorrhizal-dominated forests. The significant influence of soil sieving on Rh in all forests was not observed during incubation when glucose was not added. After adding glucose, the Rh in the sieved soils on the 5th day of incubation was averaged 27.2% lower than that in intact soils in ECM forests. On the 27th day it was 22.1% lower in the Pinus massoniana forest, but 78.0% higher in the Castanea mollissima forest. Strong relationships were detected between Rh in sieved and intact soils (r2 = 0.888), and in soils both with and without the addition of glucose (r2 = 0.827). The measured soil variables explained 74.7% and 49.7% of the variation in Rh on the 5th and 27th day of incubation, and the role of soil nutrients and microbial PLFA groups in regulating Rh varied temporally. Our findings suggest that plant mycorrhizal types influenced the role of increased C availability to microbes in regulating the response of Rh to sieving in forest ecosystems.

Habitat Significantly Affect CWD Decomposition but No Home-Field Advantage of the Decomposition Found in a Subtropical Forest, China

The home-field advantage (HFA) effect has been reported to occur in coarse woody debris (CWD) and litter. It is thought that the HFA effect may be due to the specialization of decomposers in their original habitats. However, the relative contribution of microorganisms, particularly fungi and bacteria, to deadwood decomposition is unclear because of differences in their functional at-tributes and carbon requirements, and the microorganisms that drive the HFA effect of deadwood are also unclear. Here, we analysed a dataset of microbial PLFA and substrate properties collected from the soil and CWD of two subtropical trees, Cryptomeria japonica and Platycarya strobilacea, from forests dominated by one or the other of the two species, with both species present in the forests. Our results showed that habitat and tree types all significantly affected CWD respiration rates, the CWD respiration rates were significantly higher in the deciduous broadleaf forests (DBF) than in the coniferous forest (CF) regardless of tree types, but no a large HFA of CWD decomposition found (HFA index was 4.75). Most biomarkers indicated bacteria and fungi were more abundant in the DBF than in the CF, and the concentration of microbial PLFAs was higher in Platycarya strobilacea than in Cryptomeria japonica. In addition, the relative abundance of fungi and soil B/F were remarkably positively correlated with CWD respiration, indicating that fungi may be the primary decomposers of CWD. In conclusion, our work highlights the importance of interactions between the three primary drivers (environment, substrate quality and microbes) on CWD decomposition.

Oat, corncockle, and lupine growth affects resin‐extractable soil phosphorus and soil microbial properties differently#

AbstractBackgroundImproved use of legacy phosphorus (P) in agricultural soils is requested to reduce the need for P fertilizers. Adapted use of cover crops (CCs) may be a promising tool to support this.AimWe estimated the P allocation to roots and shoots of oat (Avena sativa, cv Posedion), corncockle (Agrostemma githago), and lupine (Lupinus angustifolius, cv Iris) and their effect on soil enzyme activity, microbial community structure, and indices of plant‐available soil P.MethodsWe grew the CCs in pots on soils with low‐ and medium‐P status. After 40 days, we measured P, N, and C uptake in shoots and roots; soil microbial C, N, and P; and pH and inorganic P extracted with water (PH2O) and anion‐exchange resins (Presin). Soil microbial activity and community structure were assessed by determining phosphomono‐ and phosphodiesterase, β‐glucosidase, and N‐acetyl‐glucosaminidase activity and by extraction of phospholipid and neutral lipid fatty acids (PLFAs and NFLAs).ResultsCorncockle and lupine took up similar amounts of P, but corncockle had an almost fourfold higher concentration of P. In the low‐P soil, the activity of phosphomonoesterase and soil microbial biomass (total microbial PLFA) were higher after lupine. CCs did not affect PH2O, but after corncockle, Presin was reduced in the medium‐P soil. Oat enhanced the presence of arbuscular mycorrhizal fungi in soil.ConclusionsOur results thus suggest that CC species with different P uptake and P uptake strategies can modify aspects in soil of potential importance for the P supply of the following main crop.

Land Consolidation with Seedling Cultivation Could Decrease Soil Microbial PLFA Diversity

The impact of land consolidation on the soil microbial PLFA diversity is of great importance for understanding the effective arable land usage, improving agricultural ecological conditions and environment. In this study, we collected the soil samples (0–20 cm) in experimental plots with 0 (Z0), 1 (Z1a) and 4 (Z4a) years of land consolidation in the forest station of Ningbo City, Zhejiang Province, southeastern China. The results were analyzed using ANOVA for randomized block design. Compared with control (Z0), the soil pH value under Z1a treatment increased by 14.6%, soil organic carbon (SOC) content decreased by 65.4%, so did the PLFA contents and relative abundance of all the microbial PLFA diversity (P < 0.05), respectively. Meanwhile, for the Z1a treatment, the ratio of fungi to bacteria (F/B) significantly decreased by 35.9% (P < 0.05), while the ratio of Gram-positive bacteria to Gram-negative bacteria (G+/G−) signific antly increased by 56.1%. This was strongly related to the increased soil pH values and the decrease of SOC. The Shannon index (H) and evenness index (E) of soil microbial PLFA diversity were significantly decreased after land consolidation (P < 0.05). Compared to the Z1 treatment, the microbial PLFA diversity was improved slightly. Therefore, the land consolidation could significantly affect the composition of soil microbial PLFA diversity, and decrease the soil ecosystem stability.

FLEXIBLE SOIL MICROBIAL CARBON METABOLISM ACROSS AN ASIAN ELEVATION GRADIENT

ABSTRACTThe function and change of global soil carbon (C) reserves in natural ecosystems are key regulators of future carbon-climate coupling. Microbes play a critical role in soil carbon cycling and yet there is poor understanding of their roles and C metabolism flexibility in many ecosystems. We wanted to determine whether vegetation type and climate zone influence soil microbial community composition (fungi and bacteria) and carbon resource preference. We used a biomarker (phospholipid fatty acids, PLFAs), natural abundance 13C and 14C probing approach to measure soil microbial composition and C resource use, along a 1900–4167-m elevation gradient on Mount Gongga (7556 m asl), China. Mount Gongga has a vertical mean annual temperature gradient of 1.2–10.1°C and a diversity of typical vegetation zones in the Tibetan Plateau. Soils were sampled at 10 locations along the gradient capturing distinct vegetation types and climate zones from lowland subtropical-forest to alpine-meadow. PLFA results showed that microbial communities were composed of 2.1–51.7% bacteria and 2.0–23.2% fungi across the elevation gradient. Microbial biomass was higher and the ratio of soil fungi to bacteria (F/B) was lower in forest soils compared to meadow soils. δ13C varied between −33‰ to −17‰ with C3 plant carbon sources dominant across the gradient. Soil organic carbon (SOC) turnover did not vary among three soils we measured from three forest types (i.e., evergreen broadleaved subtropical, mixed temperate, coniferous alpine) and dissolved organic carbon (DOC) turnover decreased with soil elevation. Forest soil microbial PLFA 14C and δ13C measurements showed that forest type and climate were related to different microbial C use. The 14C values of microbial PLFAs i15, a15, 16:1, br17 decreased with elevation while those of C16:0, cyC17, and cyC19 did not show much difference among three forest ecosystems. Bacteria and bacillus represented by C16:1 and brC17 showed considerable microbial C metabolism flexibility and tended to use ancient carbon at higher altitudes. Anaerobes represented by cyC17 and cyC19 showed stronger C metabolism selectivity. Our findings reveal specific C source differences between and within soil microbial groups along elevation gradients.

Nutrient limitation may induce microbial mining for resources from persistent soil organic matter.

Fungi and bacteria are the two principal microbial groups in soil, responsible for the breakdown of organic matter (OM). The relative contribution of fungi and bacteria to decomposition is thought to impact biogeochemical cycling at the ecosystem scale, whereby bacterially dominated decomposition supports the fast turnover of easily available substrates, whereas fungal-dominated decomposition leads to the slower turnover of more complex OM. However, empirical support for this is lacking. We used soils from a detritus input and removal treatment experiment in an old-growth coniferous forest, where above- and belowground litter inputs have been manipulated for 20yr. These manipulations have generated variation in OM quality, as defined by energetic content and proxied as respiration per g soil organic matter (SOM) and the δ13 C signature in respired CO2 and microbial PLFAs. Respiration per g SOM reflects the availability and lability of C substrate to microorganisms, and the δ13 C signature indicates whether the C used by microorganisms is plant derived and higher quality (more δ13 C depleted) or more microbially processed and lower quality (more δ13 C enriched). Surprisingly, higher quality C did not disproportionately benefit bacterial decomposers. Both fungal and bacterial growth increased with C quality, with no systematic change in the fungal-to-bacterial growth ratio, reflecting the relative contribution of fungi and bacteria to decomposition. There was also no difference in the quality of C targeted by bacterial and fungal decomposers either for catabolism or anabolism. Interestingly, respired CO2 was more δ13 C enriched than soil C, suggesting preferential use of more microbially processed C, despite its lower quality. Gross N mineralization and consumption were also unaffected by differences in the ratio of fungal-to-bacterial growth. However, the ratio of C to gross N mineralization was lower than the average C/N of SOM, meaning that microorganisms specifically targeted N-rich components of OM, indicative of selective microbial N-mining. Consistent with the δ13 C data, this reinforces evidence for the use of more microbially processed OM with a lower C/N ratio, rather than plant-derived OM. These results challenge the widely held assumption that microorganisms favor high-quality C sources and suggest that there is a trade-off in OM use that may be related to the growth-limiting factor for microorganisms in the ecosystem.

Can heavy metal pollution induce bacterial resistance to heavy metals and antibiotics in soils from an ancient land-mine?

Microbial resistance to antibiotics is a growing challenge to human health. Recent evidence has indicated that antibiotic resistance can be co-selected for by exposure to heavy metals in agricultural soils. It remains unknown if this is a concern in other environments contaminated by metals. We here investigated soil microbial activities, composition and tolerance to heavy metals and antibiotics in a mining soil survey. We found that microbial respiration, growth, and biomass were affected by available metal concentrations. Most of the variation in microbial PLFA composition was explained by differences in heavy metal and pH. Additionally, pollution-induced bacterial community tolerance to toxicants including Cu, Pb, Zn, tetracycline and vancomycin was determined. Although only bacterial tolerance to Pb increased with higher levels of metals, the links between bacterial metal tolerance and soil metal concentrations were clear when considered together with previously published reports, suggesting that bacterial metal tolerance were universally elevated in the surveyed soils. The induced levels of heavy metal tolerance coincided with elevated levels of tolerance to vancomycin, but not to tetracycline. Our study showed that heavy metals can co-select for resistance to clinically important antibiotics also in ecosystems without manure input or antibiotic pollution.

Evidence of rapid non-targeted effects of cycloheximide on soil bacteria using 13C-PLFA analysis

Stable isotope probing of phospholipid fatty acids (PLFA-SIP) is useful when studying bacterial contributions to soil processes, and it is an effective way to separate fungal and bacterial activity by linking 13C enrichment to specific PLFAs. Distinguishing bacterial contributions to soil processes often employs selective inhibitors; however, studies demonstrating their efficacy when using PLFA-SIP are less common. Here, we determined the effect of the fungal inhibitor cycloheximide (4.8 mg g−1 dry soil) and the bacterial inhibitor bronopol (0.48 mg g−1 dry soil) on microbial communities white spruce [Picea glauca (Moench) Voss] forest floor by measuring the uptake of 13C-enriched glucose (2 mg g−1 dry soil) in microbial PLFAs. We targeted [13C]glucose uptake by the bacterial community conditioned to a stable soil environment of 23 °C for over 2 wk rather than new bacteria generated from active colony growth caused by glucose addition. Nearly all bacterial PLFAs exhibited pronounced inhibition of 13C enrichment in the presence of bronopol. Limited inhibition of 13C enrichment in the presence of cycloheximide was observed as bacterial PLFA affected by cycloheximide had roughly one third less 13C enrichment than samples emended with [13C]glucose alone. Inhibitory effects only reduced 13C enrichment and did not affect total PLFA concentrations, implying that the inhibitors in the concentrations applied were impeding bacterial activity without causing cell death. Based on this work, we conclude that bronopol is an effective inhibitor for bacteria. Additionally, non-targeted effects of cycloheximide on soil bacteria must be accounted for when it is used in soil incubations.

Soil chemical and biological fertility, microbial community structure and dynamics in successive and fallow sugarcane planting systems

ABSTRACTSugarcane yields are declining under successive planting (monoculture) compared to other planting systems in Florida Histosols. To evaluate soil properties related to the sugarcane yield decline, an on-farm study was conducted on soil chemical, biological, and microbial indicators variation with soil samples collected from successive green cane or burnt cane harvest, flooded fallow, and rice and sweetcorn rotation planting sites. Overall, harvest residue incorporated in the soil in green cane harvest and corn rotation increased organic matter, total carbon and C:N ratios which resulted in higher microbial biomass parameters and total PLFA biomass. However, successive planting with burnt cane harvest reduced total soil carbon and hence microbial biomass. Findings suggested that these parameters should be considered for further research to determine specific causes of sugarcane yield decline in successive planting.

Rice straw serves as additional carbon source for rhizosphere microorganisms and reduces root exudate consumption

Straw application is a common agricultural fertilisation practice, providing an additional carbon and nutrient source for soil microorganisms. We investigated the influence of rice straw application on root exudate consuming microorganisms in the rhizosphere of Zea mays based on 13CO2 pulse labelling and phospholipid fatty acid stable isotope probing (PLFA-SIP) in a paddy soil under rice-maize crop rotation. The application of straw decreased the labelling of microbial PLFAs in the rhizosphere of 30 and 40 day old maize plants by 70% compared to treatments without straw. This decrease could partially be explained by a lower rate of CO2 assimilation of the plant in the presence of rice straw. In addition, the uptake of root exudates by rhizosphere organisms was decreased due to the presence of the rice straw, which serves as an additional carbon source for these microorganisms.

Soil net methane uptake rates in response to short-term litter input change in a coniferous forest ecosystem of central China

The uptake of CH4 by well-drained soil plays a vital role in mitigating the atmospheric CH4, but the impacts of shift in plant litter input on uptake of CH4 and the underlying mechanism are not fully understood. Here, we conducted in situ measurements of soil CH4 flux rates monthly throughout the year after the short-term litter input manipulations (i.e. Detritus Input and Removal Treatment-DIRT: control, CK; double litter, DL; no litter, NL; no roots, NR; and no aboveground litter and no roots, NRNL) in a coniferous forest (Platycladus orientalis (Linn.) Franco) ecosystem in subtropical China. The associated microclimates, soil properties and microbial PLFAs were also measured. Our results showed that soils acted as CH4 sink in all litter manipulation treatments, and the CH4 sink capacity significantly differed under litter manipulation treatments. Based on annual average values, net CH4 uptake rates decreased by 37.7 ± 4.9% and 41.7 ± 5.8% in the NL and NRNL treatments (i.e. litter layer removal), respectively, compared to the CK treatment. Thus, the net CH4 uptake induced by litter layer approximately accounted for 37.7 ± 4.9% of the total net CH4 uptake rate. The net CH4 uptake rate was not significantly influenced by the root exclusion (NR) treatment. In contrast, the effect of litter addition on net CH4 uptake rate was strongly depended on soil water content. During the dry season, litter addition did not significantly affect net CH4 uptake rate. In contrast, during the wet season, the net CH4 uptake rate decreased by 47.1 ± 4.9% in the DL treatment compared to the CK treatment. There was no significant difference in net CH4 uptake rate between dry and wet season under other litter input manipulation treatments. The net CH4 uptake rate was positively correlated with the abundance of methanotrophic bacteria across all litter input manipulation treatments, whereas the significant negative relationship between net CH4 uptake rate and water filled pore space (WFPS) was only found in the DL treatment. Overall, our results suggest that aboveground organic layer (i.e. litter) is more important in regulating the soils acting as atmospheric CH4 sink than roots, while the regulating function primarily depends on soil dry/wet conditions and the abundance of methanotrophic bacteria.