Carbon use efficiency (CUE) is being intensively applied to quantify carbon (C) cycling processes from microbial cell to global scales. Energy use efficiency (EUE) is at least as important as the CUE because (i) microorganisms use organic C mainly as an energy source and not as elemental C per se, and (ii) microbial growth and maintenance are limited by energy, but not by C as a structural element. We conceptualize and review the importance of EUE by soil microorganisms and focus on (i) the energy content in organic compounds depending on the nominal oxidation state of carbon (NOSC), (ii) approaches to assess EUE, (iii) similarities and differences between CUE and EUE, and (iv) discuss mechanisms responsible for lower EUE compared to CUE. The energy content per C atom (enthalpy of combustion, the total energy stored in a compound) in organic compounds is very closely (R 2 = 0.98) positively related to NOSC and increases by 108 kJ mol −1 C per one NOSC unit. For the first time we assessed the NOSC of microbial biomass in soil (−0.52) and calculated the corresponding energy content of −510 kJ mol −1 C. We linked CUE and EUE considering the NOSC of microbial biomass and element compositions of substrates utilized by microorganisms. The mean microbial EUE (0.32–0.35) is 18% lower than CUE (0.41) using glucose as a substrate. This definitely indicates that microbial growth is limited by energy relative to C. Based on the comparison of a broad range of processes of C and energy utilization for cell growth and maintenance, as well as database of experimental CUE from various compounds, we clearly explained five mechanisms and main factors why EUE is lower than CUE. The two main mechanisms behind lower EUE versus CUE are: (i) microbial recycling: C can be microbially recycled, whereas energy is always utilized only once, and (ii) chemical reduction of organic and inorganic compounds: Energy is used for reduction, which is ongoing without C utilization.
Microbes play pivotal roles in soil organic matter (SOM) turnover: formation and decomposition. Organic fertilizers play crucial role for SOM accumulation, aggregate formation and influence microbial community composition and co-occurrence networks in microhabitats. Here, we investigated prokaryotic and fungal communities and their co-occurrence networks in four aggregate size classes in upland Ultisol following 27 years of mineral and/or organic fertilizer (rice straw, peanut straw, radish, or pig manure) application. Organic fertilizers and aggregate size classes have main and interactive effects on SOM content in aggregates (p < 0.001). Aggregate size classes accounted for most of the variance (43%) of SOM content, with more SOM accumulated in macroaggregates (>250 μm) than microaggregates (<250 μm). Increased aggregate size affected prokaryotic and fungal community structure by increasing Rhizobiales and decreasing Eurotiales. Solibacterales and Mortierellales were particularly abundant in small microaggregates (<53 μm) due to substrate preferences. Organic fertilizers regulate microbial community structure more than aggregate size, accounting for 41% and 29% of variance in prokaryotic and fungal communities, respectively. Pig manure exerted the strongest effect on SOM content and aggregation, and influenced microbial community structure more strongly than plant residues, primarily by increasing Bacillales, Gaiellales and Pezizales, and decreasing Thermogemmatisporales. This effect of pig manure was related with efficient increase of SOM content and pH. Co-occurrence network analysis revealed more positive or negative linear relationships among microbial groups in microaggregates than in macroaggregates, indicating stronger synergistic and antagonistic microbial interactions in microaggregates with fewer favorable niches (higher recalcitrant SOM and less labile SOM). Thermogemmatisporales was identified as the most influential keystone taxon (relative abundance ∼4.9%) in soil, and its abundance rapidly diminished with increasing SOM content in macro- and microaggregates. Thus, microbial community structure is dependent on aggregate size, and this should be considered during sampling. Overall, long-term pig manure amendment increased the SOM content and aggregation, altering prokaryotic and fungal community structure and keystone taxa.
Indonesia lost more tropical forest than all of Brazil in 2012, mainly driven by the rubber, oil palm, and timber industries. Nonetheless, the effects of converting forest to oil palm and rubber plantations on soil organic carbon (SOC) stocks remain unclear. We analyzed SOC losses after lowland rainforest conversion to oil palm, intensive rubber, and extensive rubber plantations in Jambi Province on Sumatra Island. The focus was on two processes: (1) erosion and (2) decomposition of soil organic matter. Carbon contents in the Ah horizon under oil palm and rubber plantations were strongly reduced up to 70% and 62%, respectively. The decrease was lower under extensive rubber plantations (41%). On average, converting forest to plantations led to a loss of 10 Mg C ha(-1) after about 15 years of conversion. The C content in the subsoil was similar under the forest and the plantations. We therefore assumed that a shift to higher δ(13) C values in plantation subsoil corresponds to the losses from the upper soil layer by erosion. Erosion was estimated by comparing the δ(13) C profiles in the soils under forest and under plantations. The estimated erosion was the strongest in oil palm (35 ± 8 cm) and rubber (33 ± 10 cm) plantations. The (13) C enrichment of SOC used as a proxy of its turnover indicates a decrease of SOC decomposition rate in the Ah horizon under oil palm plantations after forest conversion. Nonetheless, based on the lack of C input from litter, we expect further losses of SOC in oil palm plantations, which are a less sustainable land use compared to rubber plantations. We conclude that δ(13) C depth profiles may be a powerful tool to disentangle soil erosion and SOC mineralization after the conversion of natural ecosystems conversion to intensive plantations when soils show gradual increase of δ(13) C values with depth.
No abstract is provided for this article.
&lt;p&gt;Although most organic matter (OM) in soil is mineralized by microorganisms, the nonmicrobial processes, e.g., Fenton reactions and photo-degradation, strongly contribute to OM decomposition and CO&lt;sub&gt;2&lt;/sub&gt; emission and are the chemical background of many biotic transformations. Fenton oxidation is a catalytic reaction chain of hydrogen peroxide (H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt;) with ferrous iron (Fe(II)) and Fe (oxyhydr)oxides that generates highly reactive hydroxyl radicals (HO&lt;sup&gt;&amp;#8226;&lt;/sup&gt;) oxidizing OM to CO&lt;sub&gt;2&lt;/sub&gt;. Reactive Fe (oxyhydr)oxides store at least one quarter (~600 Gt) of organic C in soil, which may be subjected to Fenton reactions in which nano-sized Fe (oxyhydr)oxides act as nanocatalysts. The Fenton mechanisms depend on the sources of reactive oxygen species (ROS): O&lt;sub&gt;2&lt;/sub&gt;&lt;sup&gt;&amp;#8226;&amp;#8722;&lt;/sup&gt;, H&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;2&lt;/sub&gt; and HO&lt;sup&gt;&amp;#8226;&lt;/sup&gt;. Because microorganisms continuously produce ROS, biotic Fenton chemistry is ubiquitous in all soils, especially with strong UV radiation, fluctuating O&lt;sub&gt;2&lt;/sub&gt; concentrations and redox, microbial hotspots such as rhizosphere and detritusphere, and high contents of Fe (oxyhydr)oxides. Charcoal and biochar catalyze ROS formation in soil as an electron shuttle or by electron transfer from the valence to the conduction band under UV irradiation. Despite the extremely short lifetime (from nanoseconds to a few days), ROS are continuously produced and sustain the ubiquity of chelators and Fe(III) reduction. For the first time we calculated the fundamental Eh-pH diagrams for ROS species and showed their relevance for Fenton reactions under soil conditions. HO&lt;sup&gt;&amp;#8226;&lt;/sup&gt; as one of the most powerful oxidants (E&lt;sup&gt;o&lt;/sup&gt; = 2.8 V) provides the most energy release from Fenton reactions in soil. In some ecosystems (hot deserts; red soils in the tropics and wet subtropics) Fenton reactions contribute to OM oxidation to 30% and even exceed 50% of total CO&lt;sub&gt;2&lt;/sub&gt; emissions. Fenton reactions are omnipresent and play a dual role for soil C cycling: stimulate OM mineralization (including the most stable pools) and facilitate long-term C stabilization due to the increased recalcitrance of remaining OM and organo-mineral complex formation. Summarizing, Fenton reactions and their effects on OM decomposition and formation are an emerging research field that explains the chemical background of many oxidative enzymatic processes, may crucially change our views on C, energy and nutrient cycling in soils.&lt;/p&gt;
Despite soil microorganisms spend most of their lifetime in a state of dormancy, they are quickly activated by substrate input and easily switch to growth. As both the dsDNA- and RNA- contents increase during microbial growth, the RNA:dsDNA ratio reflects a promising predictor, whether the response of a microbial community to environmental changes is due to an increase in population (by dsDNA) or due to an increase in activity (by RNA). This prediction of the RNA:dsDNA ratio can be accomplished by the comparison of microbial incubation approaches with and without addition of easily available substrates. We exhibited the RNA:dsDNA ratios for four contrasting soil types during substrate-induced growth. Overall, after glucose addition, a strong increase of dsDNA and RNA contents were determined in most of the soil types during 72 h of incubation. Furthermore, we identified distinct temporal soil-specific RNA:dsDNA patterns. The dsDNA- and RNA-contents yielded 26–174 and 0.3–30 µg g-1 soil, respectively. The soil texture was strongly associated with the reduction of RNA recovery, by means of an exponential decrease of RNA-content with increasing clay content. The lower RNA recovery in virgin and arable Chernozem (>30%) compared to soil types with lower clay contents (<17% for Retisol, Luvisol and Calcisol) suggests, that the undercount of RNA yields in clayey soils biased the RNA:dsDNA ratio, and subsequently the physiological state of the microbial community is not adequately represented in soils with clay contents exceeding 30%.
Priming eAects are strong short-term changes in the turnover of soil organic matter caused by comparatively moderate treatments of the soil. In the course of priming eAects large amounts of C, N and other nutrients can be released or immobilized in soil in a very short time. These eAects have been measured in many field and laboratory experiments; however, only a few of the studies were aimed at an extended investigation of the mechanisms of such phenomena. The aim of this overview is to reveal possible causes and processes leading to priming actions using the references on agricultural ecosystems and model experiments. Multiple mechanisms and sources of released C and N are presented and summarized in Tables for positive and negative real and apparent priming eAects induced after the addition of diAerent organic and mineral substances to the soil. Soil microbial biomass plays the key role in the processes leading to the real priming eAects. The most important mechanisms for the real priming eAects are the acceleration or retardation of soil organic matter turnover due to increased activity or amount of microbial biomass. Isotopic exchange, pool substitution, and diAerent uncontrolled losses of mineralized N from the soil are responsible for the apparent N priming eAects. Other multiple mechanisms (predation, competition for nutrients between roots and microorganisms, preferred uptake, inhibition, etc.) in response to addition of diAerent substances are also discussed. These mechanisms can be distinguished from each other by the simultaneous monitoring of C and N release dynamics; its comparison with the course of microbial activity; and by the labelling of diAerent pools with 14 Co r 13 C and 15 N. Quantitative methods for describing priming eAects and their dynamics using 14 C and 15 N isotopes, as well as for non-isotopic studies are
Diverse plant communities are known to increase soil carbon (C) levels compared to monocultures, but an incomplete understanding of the underlying mechanisms of this phenomenon limits the development of strategies for optimizing soil C sequestration. We hypothesized that the identity of neighboring plants influences the amounts of C that a plant inputs into the soil, the resultant formation of soil pore architecture, and the fate of the plant's C inputs. To test this hypothesis, we combined 13CO2 plant pulse labeling with X-ray computed micro-tomography (μCT) in assessing plant-assimilated C from three species common to North American prairie: switchgrass, big bluestem, and wild bergamot. The plants were grown in a greenhouse in monoculture and in all-pair combinations. The 13C labeling was conducted so as to ensure that only one member of each pair has received 13C. The results demonstrated that greater belowground C exchange among neighboring plants enhanced inputs of plant-assimilated C into soil, suggesting that the involvement of plant community members in belowground C transfer, rather than community's diversity per se, drives rapid soil C accrual. Moreover, the magnitudes of C losses as well as properties of soil pore architecture also depend not only on the identity of the C source plant itself but also on the identities of its neighbors. These findings propose belowground interspecific C transfer as a previously overlooked mechanism for enriching and stabilizing soil C and suggest genomic and management potentials for selecting species that participate in intensive interspecific assimilate exchange in order to promote rapid and stable soil C gains.
Soil microbial communities, plant and microbial biomarkers, as well as SOC physical and chemical fractions in a subalpine forest under P addition. <br>
Under arid to semihumid climatic conditions, dissolution of primary carbonate and recrystallization with carbon (C) from soil CO 2 leads to accumulation of significant amounts of pedogenic (secondary) carbonate. Most soils of arid and semiarid regions contain a carbonate accumulation horizon, the depth of which is related to climatic conditions and properties of parent material. It remains unclear whether this carbonate migrates from the upper horizons before or after recrystallization with soil CO 2 . The aim of this study was to determine recrystallization rates during initial pedogenesis and to estimate the accumulation depth of secondary carbonate based on C isotopic exchange during secondary carbonate formation in an experiment with alternating moisture conditions. Maize grown on 1 m high loess‐filled columns was pulse labeled in 14 CO 2 atmosphere every 3 weeks. After 6 months, portions of secondary (recrystallized) CaCO 3 were determined in 5 cm segments, based on 14 C respired in the rhizosphere and subsequently incorporated into newly formed secondary carbonate. More than 80% of recrystallized carbonate (Ca 14 CO 3 ) was leached from the uppermost 15 cm of the loess column, and more than 70% of total secondary carbonate were accumulated in a depth between 15 and 50 cm. Based on the recrystallization rate calculated for the uppermost 15 cm of the loess column (1.77 ± 0.26 ⋅ 10 −5 day −1 ), between 300 and more than 1,700 years are necessary for complete decalcification of the upper 15 cm. Our modeled data are consistent with formation of calcic horizons under relatively humid conditions.
No abstract is provided for this article.
