Soil Microbial Communities in Natural and Managed Cloud Montane Forests

Forest management often results in changes in soil microbial communities. To understand how forest management can change microbial communities, we studied soil microbial abundance and community structure in a natural Chamaecyparis (NCP) forest, a disturbed Chamaecyparis (DCP) forest, a secondary (regenerated) Chamaecyparis (SCP) forest and a secondary (reforested) Cryptomeria (SCD) forest. We analyzed soil microbial abundance by measuring phospholipid fatty acids (PLFAs) and microbial community structure by denaturing gradient gel electrophoresis (DGGE) in the studied forest soils. The content of the soil PLFA fungal biomarker decreased from NCP to SCP, DCP and SCD forest soils, associated with the degree of disturbance of forest management. The ratio of soil Gram positive–to-negative bacteria and the stress index (16:1ω7t to 16:1ω7c) increased from NCP to SCP and DCP soils; thus, disturbed forests except for SCD showed increased soil microbial stress. Principal component analysis of soil microbial groups by PLFAs separated the four forest soils into three clusters: NCP, DCP and SCP, and SCD soil. The DGGE analysis showed no difference in the microbial community structure for NCP, DCP and SCP soils, but the community structure differed between SCD and the three other forest soils. In cloud montane forests, disturbance due to forest management had only a slight influence on the soil microbial community, whereas reforestation with different species largely changed the soil microbial community structure

The Effect of Re-Planting Trees on Soil Microbial Communities in a Wildfire-Induced Subalpine Grassland

Wildfire often causes tremendous changes in ecosystems, particularly in subalpine and alpine areas, which are vulnerable due to severe climate conditions such as cold temperature and strong wind. This study aimed to clarify the effect of tree re-planting on ecosystem services such as the soil microbial community after several decades. We compared the re-planted forest and grassland with the mature forest as a reference in terms of soil microbial biomass C and N (Cmic and Nmic), enzyme activities, phospholipid fatty acids (PLFA) composition, and denaturing gradient gel electrophoresis (DGGE). The Cmic and Nmic did not differ among the grassland, re-planted forest and mature forest soil; however, ratios of Cmic/Corg and Nmic/Ntot decreased from the grassland to re-planted forest and mature forest soil. The total PLFAs and those attributed to bacteria and Gram-positive and Gram-negative bacteria did not differ between the re-planted forest and grassland soil. Principle component analysis of the PLFA content separated the grassland from re-planted forest and mature forest soil. Similarly, DGGE analysis revealed changes in both bacterial and fungal community structures with changes in vegetation. Our results suggest that the microbial community structure changes with the re-planting of trees after a fire event in this subalpine area. Recovery of the soil microbial community to the original state in a fire-damaged site in a subalpine area may require decades, even under a re-planted forest

Relationship between Mineral Soil Surface Area and the Biological Degradation of Biosolids Added to Soil

Geochemical and biological processes that operate in the soil matrix and on the soil surface are important to the degradation of biosolids in soil. Due to the large surface area of soils it is assumed that the microbial ecology is associated with mineral soil surface area. The total mineral surface areas were determined for soils from eight different fields selected from a long term study (1972–2006) of annual biosolids application to 41 fields in central Illinois varying in size from 3.6 to 66 ha. The surface areas for the soils varied from 1 to 9 m2/g of soil. The biological degradation rates for the eight soils were determined using a biological degradation rate model (DRM) and varied from 0.02 to 0.20/year−1. Regression analysis revealed that the degradation rate was positively associated with mineral soil surface area (1 m2/g produces 0.018 year−1 increase in the degradation rate). The annual soil sequestration rate was calculated to increase from 1% to 6% when the soil total surface area increased from 1 to 9 m2/g of soil. Therefore, land application of biosolids is an effective way to enhance carbon sequestration in soils and reduce greenhouse gas emissions

Selection of reliable reference genes for quantitative RT-PCR in garlic under salt stress

Quantitative real-time reverse-transcriptase PCR (qRT-PCR) has been frequently used for detecting gene expression. To obtain reliable results, selection of suitable reference genes is a fundamental and necessary step. Garlic (Allium sativum), a member from Alliaceae family, has been used both as a food flavoring and as a traditional medicine. In the present study, garlic plants were exposed to salt stress (200 mM NaCl) for 0, 1, 4 and 12 h, and garlic roots, bulbs, and leaves were harvested for subsequent analysis. The expression stability of eight candidate reference genes, eukaryotic translation initiation factor 4α (eIF-4α), actin (ACTIN), tubulin β-7 (TUB7), TAP42-interacting protein of 41 kDa (TIP41), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), SAND family protein (SAND), elongation factor 1 alpha (EF-1α), and protein phosphatase 2A (PP2A) were evaluated by geNorm, NormFinder, and BestKeeper. All genes tested displayed variable expression profiles under salt stress. In the leaf and root group, ACTIN was the best reference gene for normalizing gene expression. In garlic clove, ACTIN and SAND were the least variable, and were suitable for gene expression studies under salt stress; these two genes also performed well in all samples tested. Based on our results, we recommend that it is essential to use specific reference genes in different situations to obtain accurate results. Using a combination of multiple stable reference genes, such as ACTIN and SAND, to normalize gene expression is encouraged. The results from the study will be beneficial for accurate determination of gene expression in garlic and other plants

Characterization of Phosphorus in Subtropical Coastal Sand Dune Forest Soils

Continuous research into the availability of phosphorus (P) in forest soil is critical for the sustainable management of forest ecosystems. In this study, we used sequential chemical extraction and 31P-nuclear magnetic resonance spectroscopy (31P-NMR) to evaluate the form and distribution of inorganic P (Pi) and organic P (Po) in Casuarina forest soils of a subtropical coastal sand dune in Houlong, Taiwan. The soil samples were collected from humic (+2⁻0 cm) and mineral layers (mineral-I: 0⁻10, mineral-II: 10⁻20 cm) at two topographic locations (upland and lowland) with different elevations. Sequential chemical extraction revealed that the NaOH-Po fraction, as moderately recalcitrant P, was the dominant form in humic and mineral-I layers in both upland and lowland soils, whereas the cHCl-Pi fraction was the dominant form in the mineral-II layer. The resistant P content, including NaOH-Pi, HCl-Pi, cHCl-Pi, and cHCl-Po fractions, was higher in the upland than in the lowland. However, the labile P content, NaHCO3-Po, showed the opposite pattern. The content of resistant Pi (NaOH-Pi, HCl-Pi, and cHCl-Pi) increased significantly with depth, but that of labile Pi (resin-Pi and NaHCO3-Pi) and recalcitrant Po (NaHCO3-Po, NaOH-Po, and cHCl-Po) decreased significantly with depth at both locations. 31P-NMR spectroscopy revealed inorganic orthophosphate and monoesters-P as the major forms in this area. The proportions of Pi and Po evaluated by sequential chemical extraction and 31P-NMR spectroscopy were basically consistent. The results indicate that the soils were in weathered conditions. Furthermore, the P distribution and forms in this coastal sand dune landscape significantly differed between the upland and lowland because of the variation in elevation and eolian aggradation effects

Traditional manual tillage significantly affects soil redistribution and CO2 emission in agricultural plots on the Loess Plateau

Traditional manual tillage using hand tools is widely used by local farmers in hilly and mountainous regions in China and many South-east Asian countries. Manual tillage could result in severe soil erosion, redistributing slopes from upslope areas (erosion) to lower slopes (deposition). This soil redistribution process may potentially affect the soil carbon cycle, but few studies have quantified soil CO2 emission under different manual tillage practices. In the present study we evaluated the soil redistribution and its effects on in situ CO2 emission as affected by manual tillage of different intensities on three short slopes representing typical cultivated landscapes on the Loess Plateau. Soils were removed at 2, 6 and 10 cm depths by three types of hand tools, namely a hoe, mattock and spade respectively, from the upslope and subsequently accumulated at the downslope to simulate soil erosion and deposition processes by traditional manual tillage. Across the tilled hillslopes, soil CO2 emission was reduced at sites of erosion but enhanced at sites of deposition. Tillage with greater intensity (i.e. hoeing < mattocking < spading) resulted in greater change in CO2 emission. This change in soil CO2 emission was largely associated with the depletion of soil organic carbon (SOC) stocks at erosion sites and the increments of SOC available for decomposition at deposition sites. Moreover, with increasing tillage intensity, soil redistribution by manual tillage shifted the hillslope from a C sink to C neutral or even a C source. Furthermore, manual tillage resulted in substantial changes in soil CO2 emission and redistributed soil in amounts that dwarf animal-powered tillage. The results of the present study imply that manual tillage-induced soil redistribution could have a large effect on the C balance across the local landscape and therefore may have considerable implications for estimates of regional and global C budgets