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Summary Corals and macroalgae release large quantities of dissolved organic matter (DOM), one of the largest sources of organic matter produced on coral reefs. By rapidly taking up DOM and transforming it into particulate detritus, coral reef sponges are proposed to play a key role in transferring the energy and nutrients in DOM to higher trophic levels via the recently discovered sponge loop. DOM released by corals and algae differs in quality and composition, but the influence of these different DOM sources on recycling by the sponge loop has not been investigated. Here, we used stable isotope pulse‐chase experiments to compare the processing of naturally sourced coral‐ and algal‐derived DOM by three Red Sea coral reef sponge species: Chondrilla sacciformis, Hemimycale arabica and Mycale fistulifera. Incubation experiments were conducted to trace 13C‐ and 15N‐enriched coral‐ and algal‐derived DOM into the sponge tissue and detritus. Incorporation of 13C into specific phospholipid‐derived fatty acids (PLFAs) was used to differentiate DOM assimilation within the sponge holobiont (i.e. the sponge host vs. its associated bacteria). All sponges assimilated both coral‐ and algal‐derived DOM, but incorporation rates were significantly higher for algal‐derived DOM. The two DOM sources were also processed differently by the sponge holobiont. Algal‐derived DOM was incorporated into bacteria‐specific PLFAs at a higher rate while coral‐derived DOM was more readily incorporated into sponge‐specific PLFAs. A substantial fraction of the dissolved organic carbon (C) and nitrogen (N) assimilated by the sponges was subsequently converted into and released as particulate detritus (15–24% C and 27–49% N). However, algal‐derived DOM was released as detritus at a higher rate. The higher uptake and transformation rates of algal‐ compared with coral‐derived DOM suggest that reef community phase shifts from coral to algal dominance may stimulate DOM cycling through the sponge loop with potential consequences for coral reef biogeochemical cycles and food webs. Lay Summary

Bacteria have evolved a defense system to resist external stressors, such as heat, pH, and salt, so as to facilitate survival in changing or harsh environments. However, the specific mechanisms by which bacteria respond to such environmental changes are not completely elucidated. Here, we used halotolerant bacteria as a model to understand the mechanism conferring high tolerance to NaCl. We screened for genes related to halotolerance in Halomonas socia, which can provide guidance for practical application. Phospholipid fatty acid analysis showed that H. socia cultured under high osmotic pressure produced a high portion of cyclopropane fatty acid derivatives, encoded by the cyclopropane-fatty acid-acyl phospholipid synthase gene (cfa). Therefore, H. socia cfa was cloned and introduced into Escherichia coli for expression. The cfa-overexpressing E. coli strain showed better growth, compared with the control strain under normal cultivation condition as well as under osmotic pressure (> 3% salinity). Moreover, the cfa-overexpressing E. coli strain showed 1.58-, 1.78-, 3.3-, and 2.19-fold higher growth than the control strain in the presence of the inhibitors furfural, 4-hydroxybenzaldehyde, vanillin, and acetate from lignocellulosic biomass pretreatment, respectively. From a practical application perspective, cfa was co-expressed in E. coli with the polyhydroxyalkanoate (PHA) synthetic operon of Ralstonia eutropha using synthetic and biosugar media, resulting in a 1.5-fold higher in PHA production than that of the control strain. Overall, this study demonstrates the potential of the cfa gene to boost cell growth and production even in heterologous strains under stress conditions.

AIMS: This study aimed to determine the influence of tree species on soil microbial community structure. METHODS: We conducted a litter and root manipulation and a short-term nitrogen (N) addition experiment in 19-year-old broadleaf Mytilaria laosensis (Hamamelidaceae) and coniferous Chinese fir (Cunninghamia lanceolata) plantations in subtropical China. Phospholipid fatty acid (PLFA) analysis was used to examine treatment effects on soil microbial community structure. Redundancy analysis (RDA) was performed to determine the relationships between individual PLFAs and soil properties (soil pH, carbon (C) and N concentration and C:N ratio). RESULTS: Soil C:N ratio was significantly greater in M. laosensis (17.9) than in C. lanceolata (16.2). Soil C:N ratio was the key factor affecting the soil microbial community regardless of tree species and the litter, root and N treatments at our study site. The fungal biomarkers, 18:1ω9 and 18:2ω6,9 were significantly and positively related to soil C:N ratio and the abundance of bacterial lipid biomarkers was negatively related to soil C:N ratio. N addition for 8 months did not change the biomass and structure of the microbial community in M. laosensis and C. lanceolata soils. Soil nutrient availability before N addition was an important factor in determining the effect of N fertilization on soil microbial biomass and activity. PLFA analysis showed that root exclusion significantly decreased the abundance of the fungal biomarkers and increased the abundance of the Gram-positive bacteria. Rootless plots had a relatively lower Gram-positive to Gram-negative bacteria ratio and a higher fungi to bacteria ratio compared to the plots with roots under both M. laosensis and C. lanceolata. The response of arbuscular mycorrhizal fungi (16:1ω5) to root exclusion was species-specific. CONCLUSIONS: These observations suggest that soil C:N ratio was an important factor in influencing soil microbial community structure. Further studies are required to confirm the long-term effect of tree species on soil microbial community structure.

Background and aim Global nitrogen (N) deposition has been proposed to enhance phosphorus (P) limitation in various terrestrial ecosystems. The impact of N addition on soil P transformation, considering both microbial and abiotic properties, is not well understood. Methods In this study, the experiment with three levels of N addition (0 (N0, no fertilizer), 25 (N25) and 50 kg N ha −1 yr −1 (N50)) was implemented in a temperate broad-leaved forest to assess the long-term (12 years) effects of N addition on soil P fractions associated with soil properties, iron, aluminum, calcium, phospholipid fatty acids (PLFAs), and enzyme activities. Results The results indicated a significant decrease in labile P, despite of a significant increase of approximately 54.0% in available P under N addition (N50). In contrast, the moderately labile P significantly increased under N addition treatment because of the increase in organic P in less labile fractions. The redundancy analysis and mantel-test found soil pH and MBP contributed to the variation of soil P fractions. The results of structural equation model confirmed that the microbial biomass P play a key role in the transformation of soil available P into moderately and occluded P fractions. Conclusion These results suggested that the long-term addition of N decreased soil labile P and increased moderate and occluded P fractions through increasing microbial P use efficiency with increased MBP, leading to the enhancement of soil P limitation in the broad-leaved temperate forest.

Despite the importance of litter decomposition for ecosystem fertility and carbon balance, key uncertainties remain about how this fundamental process is affected by nitrogen (N) availability. Resolving such uncertainties is critical for predicting the ecosystem consequences of increased anthropogenic N deposition. Toward that end, we decomposed green leaves and senesced litter of northern pin oak ( Quercus ellipsoidalis ) in three forested stands dominated by northern pin oak or white pine ( Pinus strobus ) to compare effects of substrate N (as it differed between leaves and litter) and externally supplied N (inorganic or organic forms) on decomposition and decomposer community structure and function over four years. Asymptotic decomposition models fit the data equally well as single exponential models and allowed us to compare effects of N on both the initial decomposition rate ( k a ) and the level of asymptotic mass remaining ( A , proportion of mass remaining at which decomposition approaches zero, i.e., the fraction of slowly decomposing litter). In all sites, both substrate N and externally supplied N (regardless of form) accelerated the initial decomposition rate. Faster initial decomposition rates corresponded to higher activity of polysaccharide-degrading enzymes associated with externally supplied N and greater relative abundances of Gram-negative and Gram-positive bacteria associated with green leaves and externally supplied organic N (assessed using phospholipid fatty acid analysis, PLFA). By contrast, later in decomposition, externally supplied N slowed decomposition, increasing the fraction of slowly decomposing litter ( A ) and reducing lignin-degrading enzyme activity and relative abundances of Gram-negative and Gram-positive bacteria. Higher-N green leaves, on the other hand, had lower levels of A (a smaller slow fraction) than lower-N litter. Contrasting effects of substrate and externally supplied N during later stages of decomposition likely occurred because higher-N leaves also had considerably lower lignin, causing them to decompose more quickly throughout decomposition. In conclusion, elevated atmospheric N deposition in forest ecosystems may have contrasting effects on the dynamics of different soil carbon pools, decreasing mean residence times of active fractions in fresh litter (which would be further reduced if deposition increased litter N concentrations), while increasing those of more slowly decomposing fractions, including more processed litter.

While high soil carbon stability had been well known for biochar‐amended soils, how conversion of crop residues into biochar and subsequent biochar amendment (BA) would favor microbial carbon use and carbon sequestration had not been clearly understood. In this study, topsoil samples were collected from an upland soil and a paddy soil, both previously amended with straw and straw‐derived biochar. These samples were incubated with 13C‐labeled maize residue (LMR) for 140 days to compare carbon mineralization, metabolic quotient (qCO2), and microbial carbon use efficiency (CUE) under laboratory incubation. 13C‐phospholipid fatty acid (13C‐PLFA) was used to trace the use of substrate carbon by soil microorganisms. Comparing to straw amendment (SA), BA significantly decreased the native soil organic carbon (SOC) mineralization rates by 19.7%–20.1% and 9.2%–12.0% in the upland and paddy soils, respectively. Meanwhile, total carbon mineralization from the newly added LMR was significantly decreased by 12.9% and 11.1% in the biochar‐amended soils, compared with the straw‐amended soils from the upland and paddy sites, respectively. Furthermore, compared to non‐amended soils, the qCO2 value was unchanged in straw‐amended soils, but was notably decreased by 15.2%–18.6% and 8.9%–12.5% in biochar‐amended upland and paddy soils, respectively. Microbial CUE was significantly greater in biochar‐amended soils than in straw‐amended soils due to the increasing dominance of fungi in carbon utilization. Compared to SA, BA increased CUE by 23.0% in the upland soil and 21.2% in the paddy soil. This study suggests that BA could outperform SA in the long term to enhance the biological carbon sequestration potential of both upland and paddy soils. This could be due mainly to biochar input as a special substrate to promote microbial community evolution and increase the fungal utilization of carbon substrates, especially for the soil with lower SOC levels. This work aimed to compare the effect of crop straws and crop straw‐derived biochar amendment (BA) on microbial carbon use and carbon sequestration potential. Topsoil samples were collected from an upland soil and a paddy soil, both previously amended with straw and straw‐derived biochar, and these samples were incubated with 13C‐labelled maize residue to monitor the soil organic matter decomposition. Moreover, the metabolic quotient, microbial carbon use efficiency and 13C‐phospholipid fatty acid were analyzed. This study suggests that BA could outperform straw amendment in the long term to enhance the biological carbon sequestration potential of both upland and paddy soils.

Little is known about the path of root-derived carbon (C) into soil microbial communities in response to arbuscular mycorrhizal fungi (AMF) and nitrogen (N) fertilization. A mycorrhiza defective mutant of tomato (reduced mycorrhizal colonization: rmc ) and its mycorrhizal wild type progenitor (MYC) were used to control for the formation of AMF. 16-week continuous 13 CO 2 labeling was performed to quantify the photosynthetic C allocation in active microorganisms via 13 C profiles of neutral (NLFAs) and phospholipid fatty acids (PLFAs). The 13 C incorporation into fungal biomarker (the sum of PLFA 16:1ω5c, NLFA 16:1ω5c, PLFA 18:2ω6,9) increased with time over 16 weeks, and 4.62% of totally assimilated C was incorporated into AMF. More 13 C was allocated into AMF storage compounds (NLFA 16:1ω5c, 3.1–4.1%) than hyphal biomass (PLFA 16:1ω5c, 0.12–0.25%). Furthermore, AMF symbiosis shifted microbial community composition, resulting in a lower 13 C incorporation into bacteria and saprotrophic fungi compared to rmc plants. This suggests a lower use of root-derived C by bacteria and saprotrophic fungi but preference to older C compounds as energy sources. However, N fertilization decreased AMF abundance and subsequently less root-derived C was incorporated into PLFA and NLFA 16:1ω5c in relative to unfertilized soils, due to less C allocation caused by an increased C immobilization in the aboveground biomass. Our findings suggested that root-derived C can be sequestered by AMF through storage in their reproductive organs, but the preferential C allocation to AMF might be at the expense of C flow to other microbial groups. Overall, our results confirmed that mycorrhizal plants exert a greater influence on C incorporation into bacteria and saprotrophic fungi, which, however, is highly dependent on N fertilization.

Summary Resource control over abundance, structure and functional diversity of soil microbial communities is a key determinant of soil processes and related ecosystem functioning. Copiotrophic organisms tend to be found in environments which are rich in nutrients, particularly carbon, in contrast to oligotrophs, which survive in much lower carbon concentrations. We hypothesized that microbial biomass, activity and community structure in nutrient‐poor soils of an Amazonian rain forest are limited by multiple elements in interaction. We tested this hypothesis with a fertilization experiment by adding C (as cellulose), N (as urea) and P (as phosphate) in all possible combinations to a total of 40 plots of an undisturbed tropical forest in French Guiana. After 2 years of fertilization, we measured a 47% higher biomass, a 21% increase in substrate‐induced respiration rate and a 5‐fold higher rate of decomposition of cellulose paper discs of soil microbial communities that grew in P‐fertilized plots compared to plots without P fertilization. These responses were amplified with a simultaneous C fertilization suggesting P and C colimitation of soil micro‐organisms at our study site. Moreover, P fertilization modified microbial community structure (PLFAs) to a more copiotrophic bacterial community indicated by a significant decrease in the Gram‐positive : Gram‐negative ratio. The Fungi : Bacteria ratio increased in N fertilized plots, suggesting that fungi are relatively more limited by N than bacteria. Changes in microbial community structure did not affect rates of general processes such as glucose mineralization and cellulose paper decomposition. In contrast, community level physiological profiles under P fertilization combined with either C or N fertilization or both differed strongly from all other treatments, indicating functionally different microbial communities. While P appears to be the most critical from the three major elements we manipulated, the strongest effects were observed in combination with either supplementary C or N addition in support of multiple element control on soil microbial functioning and community structure. We conclude that the soil microbial community in the studied tropical rain forest and the processes it drives is finely tuned by the relative availability in C, N and P. Any shifts in the relative abundance of these key elements may affect spatial and temporal heterogeneity in microbial community structure, their associated functions and the dynamics of C and nutrients in tropical ecosystems. Lay Summary

Soil organic matter (SOM) constitutes more than two-thirds of terrestrial carbon stocks yet there are many uncertainties about the fate of soil carbon reserves with global environmental change. Moisture, altered nutrient cycles, species shifts, growing season length or rising temperatures may alter forest primary productivity and the proportions of above and belowground biomass entering soil. We investigated SOM composition using molecular-level techniques after 20 years of detrital input and removal treatment (DIRT) at the Harvard Forest. SOM biomarkers (solvent extraction, base hydrolysis and cupric(II) oxide oxidation) and nuclear magnetic resonance (NMR) spectroscopy were used to quantify changes in SOM composition and microbial activity and community composition was assessed using phospholipid fatty acid (PLFA) analysis. Doubling aboveground litter inputs decreased soil carbon content, increased the degradation of labile SOM and enhanced the sequestration of aliphatic compounds in soil. The exclusion of belowground inputs resulted in a decrease in root-derived components and enhanced the degradation of stable SOM components such as leaf-derived aliphatic structures (cutin). The DIRT manipulations resulted in soil microbial community shifts that were attributed to the accelerated processing of specific SOM components. These results collectively reveal that a detailed molecular-level characterization of SOM can provide information on SOM compositional changes and transformations after 20 years of input manipulation in a temperate forest.

Psychrophilic bacteria, living at low and mild temperatures, can contribute significantly to our understanding of microbial responses to temperature, markedly occurring in the bacterial membrane. Here, a newly isolated strain, Pseudomonas sp. B14-6, was found to dynamically change its unsaturated fatty acid and cyclic fatty acid content depending on temperature which was revealed by phospholipid fatty acid (PLFA) analysis. Genome sequencing yielded the sequences of the genes Δ-9-fatty acid desaturase ( desA ) and cyclopropane-fatty acid-acyl-phospholipid synthase ( cfa ). Overexpression of desA in Escherichia coli led to an increase in the levels of unsaturated fatty acids, resulting in decreased membrane hydrophobicity and increased fluidity. Cfa proteins from different species were all found to promote bacterial growth, despite their sequence diversity. In conclusion, PLFA analysis and genome sequencing unraveled the temperature-related behavior of Pseudomonas sp. B14-6 and the functions of two membrane-related enzymes. Our results shed new light on temperature-dependent microbial behaviors and might allow to predict the consequences of global warming on microbial communities.