Year-long Incubation Research Articles

Temperature sensitivity of SOM decomposition is linked with a K-selected microbial community.

Temperature sensitivity (Q10 ) of soil organic matter (SOM) decomposition is a crucial parameter to predict the fate of soil carbon (C) under global warming. Nonetheless, the response pattern of Q10 to continuous warming and the underlying mechanisms are still under debate, especially considering the complex interactions between Q10 , SOM quality, and soil microorganisms. We examined the Q10 of SOM decomposition across a mean annual temperature (MAT) gradient from -1.9 to 5.1°C in temperate mixed forest ecosystems in parallel with SOM quality and bioavailability, microbial taxonomic composition, and functional genes responsible for organic carbon decomposition. Within this temperature gradient of 7.0°C, the Q10 values increased with MAT, but decreased with SOM bioavailability. The Q10 values increased with the prevalence of K-strategy of soil microbial community, which was characterized by: (i) high ratios of oligotrophic to copiotrophic taxa, (ii) ectomycorrhizal to saprotrophic fungi, (iii) functional genes responsible for degradation of recalcitrant to that of labile C, and (iv) low average 16S rRNA operon copy number. Because the recalcitrant organic matter was mainly utilized by the K-strategists, these findings independently support the carbon quality-temperature theory from the perspective of microbial taxonomic composition and functions. A year-long incubation experiment was performed to determine the response of labile and recalcitrant C pools to warming based on the two-pool model. The decomposition of recalcitrant SOM was more sensitive to increased temperature in southern warm regions, which might attribute to the dominance of K-selected microbial communities. It implies that climate warming would mobilize the larger recalcitrant pools in warm regions, exacerbating the positive feedback between increased MAT and CO2 efflux. This is the first attempt to link temperature sensitivity of SOM decomposition with microbial eco-strategies by incorporating the genetic information and disentangling the complex relationship between Q10 and soil microorganisms.

A Deeper Understanding of Carbon Decomposition in Arctic Soils

Physical parameters may help scientists extrapolate Arctic carbon soil losses from the local to the regional scale, according to the results of a yearlong incubation experiment.

Asynchronous responses of soil carbon dioxide, nitrous oxide emissions and net nitrogen mineralization to enhanced fine root input

Global environmental changes can remarkably alter the amount of fine root litter inputs to the soil; these inputs affect soil CO2 and N2O emissions and net N mineralization processes by changing C and N supply to microorganisms. However, how these C and N processes respond to the amount of fine root litter input is yet not known. In this study, a year-long incubation experiment was conducted to investigate the impacts of changes in fine root litter biomass input on soil respiration, N2O emissions, and net N mineralization. Soil samples were obtained from forests of four biomes (boreal, temperate, subtropical, and tropical), and each sample was amended with fine roots from two species (either native tree species or maize roots) with four levels of root biomass input. The cumulative CO2 emissions increased linearly with root input levels, regardless of soil and root litter types. Soil respiration responded strongly to root inputs within the first 100 days and then leveled off. Root inputs retarded soil N2O emissions and net N mineralization, and the length of delay increased with root input levels, except for temperate and subtropical soils amended with tree roots, for which N2O emission dynamics were not altered by root input. Tree roots retarded net N mineralization more intensively than maize roots except for the tropical tree roots. Cumulative N2O emissions increased linearly with root input levels in only some soil type–root species–root input level combinations. Taken together, our results suggest that increased fine root biomass production might result in a linear increase of soil C loss via heterotrophic respiration, indicating that the first-order kinetic functions that have been widely used in the soil C models are still valid for predicting C mineralization rates in response to the changes in the amount of root litter inputs. Fine roots in their initial decomposition stage could be the predominant sources of soil N2O emissions in some but not all terrestrial ecosystems. However, increased fine root input might retard net N mineralization, which might disrupt the temporal pattern of ecosystem N cycling, and thus have important consequences on plant N supply and growth.

Isotopic characterization of sequestration and transformation of plant residue carbon in relation to soil aggregation dynamics

Soil aggregates play a key role in preserving soil organic carbon (SOC). However, the mechanisms controlling aggregate formation and SOC distribution in different sizes of aggregates remain unclear. Here, we studied the dynamics of aggregate formation and associated SOC transferring among different aggregate fractions using an isotopic tracer technique (14C-labeled wheat residues). The year-long incubation results demonstrate that the wheat residue carbon applied to soil (Typic Hapludoll) was initially mainly stored in the pores between microaggregates that were agglomerated to form macroaggregates (>250μm). The wheat carbon started to transfer to the inside of microaggregates (250–53μm) after six months of the incubation. The newly formed humic acid carbon (HA14C) and fulvic acid carbon (FA14C) in the macroaggregates were 57–90% and 60–84% more than in microaggregates (250–53μm), respectively. Later, the sequestrated SOC was decomposed or chemically transformed, resulting in a decrease in the ratio of HA14C/FA14C in macroaggregates and an increase in the silt/clay fraction (<53μm). This result indicated that the SOC in the macroaggregates was vulnerable to degradation due to less protection by soil macrostructure, while it experienced a slow degradation due to strong surface adsorption or pore protection in soil microstructure. This study suggests that macroaggregates considerably control SOC turnover and thereby their stability considerably influences how much newly introduced organic carbon could be sequestrated into stable carbon pools like microaggregates. The turnover dynamics of macroaggregates provided insights into the potential of humic carbon formation that facilitates long-term carbon preservation in soil.

Does ochre have the potential to be a remedial treatment for As-contaminated soils?

Ochre is an iron oxyhydroxide-rich waste that accumulates in water bodies associated with disused mines. Laboratory experiments were conducted to examine the potential of four different ochres to be used as remedial agents for As contaminated soils. The ochres removed As from solution (200 and 500 mg L−1) in adsorption experiments at pH 3 and 8 and, when added to As contaminated soil (5% w/w) significantly reduced As release to solution. In both these experiments the highest surface area ochres performed best. The impact of ochre amendments on uptake of As from soil by plants and humans and release of As to ground water was assessed in a year-long incubation study. Ochres increased soil pH and reduced CaCl2 extractable As but had no consistent effect on plant growth, plant As uptake or As extraction in physiologically-based extraction tests. Ochre may be better used for water treatment than soil remediation.

Bacterial dynamics during yearlong spontaneous fermentation for production of ngari, a dry fermented fish product of Northeast India

Ngari is the most popular traditionally processed non-salted fish product, prepared from sun-dried small cyprinid fish Puntius sophore (Ham.) in Manipur state of Northeast India. The microbial involvement in ngari production remained uncertain due to its low moisture content and yearlong incubation in anaerobically sealed earthen pots without any significant change in total microbial count. The culture-independent PCR-DGGE analysis used during this study confirmed a drastic bacterial community structural change in comparison to its raw material. To understand the bacterial dynamics during this dry fermentation, time series samples collected over a period of nine months through destructive sampling from two indigenous ngari production centres were analysed by using both culture-dependent and culture-independent molecular methods. A total of 210 bacteria isolated from the samples were identified by amplified ribosomal DNA restriction analysis (ARDRA) based grouping and 16S rRNA gene sequence similarity analysis. The dominant bacteria were Staphylococcus cohnii subsp. cohnii (38.0%), Tetragenococcus halophilus subsp. flandriensis (16.8%), a novel phylotype related to Lactobacillus pobuzihii (7.2%), Enterococcus faecium (7.2%), Bacillus indicus (6.3%) and Staphylococcus carnosus (3.8%). Distinct bacterial dynamics with the emergence of T. halophilus at third month (106CFU/g), L. pobuzihii at sixth month (106CFU/g), S. carnosus at three to six months (104CFU/g) and B. indicus at six to nine months (105CFU/g) in both the production centres was observed during ngari fermentation. However, the other two dominant bacteria S. cohnii and E. faecium were isolated throughout the fermentation with the population of 106CFU/g and 104CFU/g respectively. Culture-independent PCR-DGGE analysis further showed the presence of additional species, in which Kocuria halotolerans and Macrococcus caseolyticus disappeared during fermentation while Clostridium irregulare and Azorhizobium caulinodans were detected throughout the fermentation. Principal component analysis showed a drastic bacterial community structural change at the sixth month of fermentation. These identified dominant bacterial cultures of T. halophilus, L. pobuzihii, S. carnosus and B. indicus could be effectively utilised for designing starter culture and optimizing fermentation technology for industrialisation of ngari production.

Testing the stability of carbon pools stored in tussock sedge meadows

Tussocks formed by Carex stricta are a relatively large carbon (C) pool in sedge meadows, but the stability of organic matter in these ecosystems is not well understood. We initiated year-long incubation experiments (22.5°C) to evaluate the CO2 and CH4 production potentials of sedge meadow substrates under field moist and inundated treatments from five sites in the Upper Midwest, USA (4 reference, 1 restored). C mineralization potentials decreased with depth (tussocks>underlying soil), and were positively correlated with macro-organic matter content and negatively with lignin. Across sites, C stored in tussocks and soil at the restoration was the least stable, suggesting that the restoration of C-storage function may take decades. Mineralization potentials were similar between field moist and inundated treatments, but inundation resulted in higher methane production, accounting for 24–51% of total carbon mineralized from tussocks. In the field however, C. stricta tussocks emitted less methane (393±76mgCH4m−2d−1) than tussock interspaces (1362±371mgCH4m−2d−1) early in the growing season; we suggest that tussock tops oxidized methane produced from deeper anoxic horizons. Our results highlight the importance of considering how microtopography modulates greenhouse gas flux from wetlands and suggests that the C stored in the older, more decomposed C. stricta tussock sedge meadow substrates (both within and between sites) is relatively stable.

LIVE AND DEAD FORAMINIFERAL FAUNAS FROM SAINT-TROPEZ CANYON (BAY OF FREJUS): OBSERVATIONS BASED ON IN SITU AND INCUBATED CORES

The impact of sedimentary processes on the live (rose- Bengal-stained) foraminiferal faunas and on the composition of dead assemblages was investigated at a 373-m-deep station in Saint-Tropez Canyon (Bay of Frejus, France). For the .150-mm fraction, biocoenoses and thanatocoenoses were investigated in two 10-cm-long cores collected with a classical Barnett multi-corer. In the 63- to 150-mm size fraction, living faunas were investigated in the first centimeter of the sediment. The first core was fixed with ethanol and rose- Bengal at the time of the sampling (the in situ core) whereas the second core was stored in a culture room during a 2.5- year-long incubation before its fauna was investigated. Both cores present similar thanatocoenoses (.150-mm size fraction) that are substantially contaminated by neritic foraminifera presumably transported from adjacent shelves. The sedimentological analysis of a third core reveals neither graded sediments nor erosional surfaces. Abundant organic remains are detected downcore in the muddy silt sediment. All these observations preclude the idea of deposition by a recent turbidite. Therefore, our canyon environment seems to behave at present as a depocenter for a rather continuous flux of fine sediment and resuspended organic matter originating from shallower areas.

Density fractionation of forest soils: methodological questions and interpretation of incubation results and turnover time in an ecosystem context

Soil organic matter (SOM) is often separated by physical means to simplify a com- plex matrix into discrete fractions. A frequent approach to isolating two or more fractions is based on differing particle densities and uses a high density liquid such as sodium polytungstate (SPT). Soil density fractions are often interpreted as organic matter pools with different carbon (C) turnover times, ranging from years to decades or centuries, and with different functional roles for C and nutrient dynamics. In this paper, we discuss the development and mechanistic basis of common density-based methods for dividing soil into distinct organic matter fractions. Further, we directly address the potential effects of dispersing soil in a high density salt solution on the recov- ered fractions and implications for data inter- pretation. Soil collected from forested sites at H. J. Andrews Experimental Forest, Oregon and Bousson Experimental Forest, Pennsylvania was separated into light and heavy fractions by floa- tation in a 1.6 g cm -3 solution of SPT. Mass balance calculations revealed that between 17% and 26% of the original bulk soil C and N content was mobilized and subsequently discarded during density fractionation for both soils. In some cases, the light isotope was preferentially mobilized during density fractionation. During a year-long incubation, mathematically recombined density fractions respired ~40% less than the bulk soil at both sites and light fraction (LF) did not always decompose more than the heavy fraction (HF). Residual amounts of tungsten (W) present even in well-rinsed fractions were enough to reduce microbial respiration by 27% compared to the control in a 90-day incubation of Oa material. However, residual W was nearly eliminated by repeated leaching over the year-long incubation, and is not likely the primary cause of the difference in respiration between summed frac- tions and bulk soil. Light fraction at Bousson, a deciduous site developed on Alfisols, had a radiocarbon-based mean residence time (MRT)

Do TSD, sex ratios, and nest characteristics influence the vulnerability of tuatara to global warming?

Tuatara ( Sphenodon punctatus) are threatened New Zealand reptiles with temperature-dependent sex determination (TSD). Higher incubation temperatures produce males, and less than 1 °C separates production of males and females. We investigated variability in nesting ecology to assess whether global warming is likely to result in increasingly male-biased populations. We examined nesting seasons during 1998/1999 and 2002/2003 in New Zealand's largest tuatara population on Stephens Island, and collected hourly temperature recordings and physical descriptions from 70 nests. Nest depths were not significantly different between years, and ranged from 10 to 230 mm from the soil surface to the top egg. Incubation temperatures in successful nests throughout the year-long incubation period ranged from 1.6 to 38.4 °C. Sex ratios of nests were correlated with incubation temperature: 64% males were produced in 1998/1999, a relatively warm season, but we predict an equal sex ratio was produced in 2002/2003. Although temperatures varied over the 2002/2003 season with respect to monthly long-term averages, 2002 was the second warmest year on record. Stephens Island supports a wide range of nesting habitat, a relatively large population of tuatara, and nest characteristics are highly variable. As such, this population is likely to be resilient to global warming in the short term because an equal sex ratio was predicted from a relatively warm season. However, most other islands where tuatara occur are smaller, have smaller populations, and have fewer open areas for nesting and/or shallower soils. These conditions are more likely to produce a male bias in hatchlings because female tuatara do not appear to vary construction of nests with respect to temperature or location. In the extreme, this could lead to the extinction of small populations.

Transformation of organic matter from maize residues into labile and humic fractions of three European soils as revealed by 13C distribution and CPMAS‐NMR spectra

SummaryThe dynamics of incorporation of fresh organic residues into the various fractions of soil organic matter have yet to be clarified in terms of chemical structures and mechanisms involved. We studied by 13C‐dilution analysis and CPMAS‐13C‐NMR spectroscopy the distribution of organic carbon from mixed or mulched maize residues into specific defined fractions such as carbohydrates and humic fractions isolated by selective extractants in a year‐long incubation of three European soils. The contents of carbohydrates in soil particle size fractions and relative δ13C values showed no retention of carbohydrates from maize but rather decomposition of those from native organic matter in the soil. By contrast, CPMAS‐13C‐NMR spectra of humic (HA) and fulvic acids (FA) extracted by alkaline solution generally indicated the transfer of maize C (mostly carbohydrates and peptides) into humic materials, whereas spectra of organic matter extracted with an acetone solution (HE) indicated solubilization of an aliphatic‐rich, hydrophobic fraction that seemed not to contain any C from maize. The abundance of 13C showed that all humic fractions behaved as a sink for C from maize residues but the FA fraction was related to the turnover of fresh organic matter more than the HA. Removal of hydrophobic components from incubated soils by acetone solution allowed a subsequent extraction of HA and, especially, FA still containing much C from maize. The combination of isotopic measurements and NMR spectra indicated that while hydrophilic compounds from maize were retained in HA and FA, hydrophobic components in the HE fraction had chemical features similar to those of humin. Our results show that the organic compounds released in soils by mineralization of fresh plant residues are stored mainly in the hydrophilic fraction of humic substances which are, in turn, stabilized against microbial degradation by the most hydrophobic humic matter. Our findings suggest that native soil humic substances contribute to the accumulation of new organic matter in soils.