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1. Metagenomic Characterization of Soil Microbial Communities in the Luquillo Experimental Forest (Puerto Rico) and Implications for Nitrogen Cycling

   https://doi.org/10.1128/AEM.00546-21  

   Karthikeyan, Smruthi; Orellana, Luis H.; Johnston, Eric R.; Hatt, Janet K.; Löffler, Frank E.; Ayala-del-Río, Héctor L.; González, Grizelle; Konstantinidis, Konstantinos T. (May 2021, Applied and Environmental Microbiology)

   Drake, Harold L. (Ed.)

   ABSTRACT The phylogenetic and functional diversities of microbial communities in tropical rainforests and how these differ from those of temperate communities remain poorly described but are directly related to the increased fluxes of greenhouse gases such as nitrous oxide (N 2 O) from the tropics. Toward closing these knowledge gaps, we analyzed replicated shotgun metagenomes representing distinct life zones and an elevation gradient from four locations in the Luquillo Experimental Forest (LEF), Puerto Rico. These soils had a distinct microbial community composition and lower species diversity compared to those of temperate grasslands or agricultural soils. In contrast to the overall distinct community composition, the relative abundances and nucleotide sequences of N 2 O reductases ( nosZ ) were highly similar between tropical forest and temperate soils. However, respiratory NO reductase ( norB ) was 2-fold more abundant in the tropical soils, which might be relatable to their greater N 2 O emissions. Nitrogen fixation ( nifH ) also showed higher relative abundance in rainforest than in temperate soils, i.e., 20% versus 0.1 to 0.3% of bacterial genomes in each soil type harbored the gene, respectively. Finally, unlike temperate soils, LEF soils showed little stratification with depth in the first 0 to 30 cm, with ∼45% of community composition differences explained solely by location. Collectively, these results advance our understanding of spatial diversity and metabolic repertoire of tropical rainforest soil communities and should facilitate future ecological studies of these ecosystems. IMPORTANCE Tropical rainforests are the largest terrestrial sinks of atmospheric CO 2 and the largest natural source of N 2 O emissions, two greenhouse gases that are critical for the climate. The microbial communities of rainforest soils that directly or indirectly, through affecting plant growth, contribute to these fluxes remain poorly described by cultured-independent methods. To close this knowledge gap, the present study applied shotgun metagenomics to samples selected from three distinct life zones within the Puerto Rico rainforest. The results advance our understanding of microbial community diversity in rainforest soils and should facilitate future studies of natural or manipulated perturbations of these critical ecosystems. 

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2. Sustained bacterial N2O reduction at acidic pH

   https://doi.org/10.1038/s41467-024-48236-x  

   He, Guang; Chen, Gao; Xie, Yongchao; Swift, Cynthia M.; Ramirez, Diana; Cha, Gyuhyon; Konstantinidis, Konstantinos T.; Radosevich, Mark; Löffler, Frank E. (May 2024, Nature Communications)

   Abstract Nitrous oxide (N₂O) is a climate-active gas with emissions predicted to increase due to agricultural intensification. Microbial reduction of N₂O to dinitrogen (N₂) is the major consumption process but microbial N₂O reduction under acidic conditions is considered negligible, albeit strongly acidic soils harbornosZgenes encoding N₂O reductase. Here, we study a co-culture derived from acidic tropical forest soil that reduces N₂O at pH 4.5. The co-culture exhibits bimodal growth with aSerratiasp. fermenting pyruvate followed by hydrogenotrophic N₂O reduction by aDesulfosporosinussp. Integrated omics and physiological characterization revealed interspecies nutritional interactions, with the pyruvate fermentingSerratiasp. supplying amino acids as essential growth factors to the N₂O-reducingDesulfosporosinussp. Thus, we demonstrate growth-linked N₂O reduction between pH 4.5 and 6, highlighting microbial N₂O reduction potential in acidic soils. 

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3. Wetting‐induced soil CO₂ emission pulses are driven by interactions among soil temperature, carbon, and nitrogen limitation in the Colorado Desert

   https://doi.org/10.1111/gcb.16669  

   Andrews, Holly M.; Krichels, Alexander H.; Homyak, Peter M.; Piper, Stephanie; Aronson, Emma L.; Botthoff, Jon; Greene, Aral C.; Jenerette, G. Darrel (March 2023, Global Change Biology)

   Abstract Warming‐induced changes in precipitation regimes, coupled with anthropogenically enhanced nitrogen (N) deposition, are likely to increase the prevalence, duration, and magnitude of soil respiration pulses following wetting via interactions among temperature and carbon (C) and N availability. Quantifying the importance of these interactive controls on soil respiration is a key challenge as pulses can be large terrestrial sources of atmospheric carbon dioxide (CO₂) over comparatively short timescales. Using an automated sensor system, we measured soil CO₂flux dynamics in the Colorado Desert—a system characterized by pronounced transitions from dry‐to‐wet soil conditions—through a multi‐year series of experimental wetting campaigns. Experimental manipulations included combinations of C and N additions across a range of ambient temperatures and across five sites varying in atmospheric N deposition. We found soil CO₂pulses following wetting were highly predictable from peak instantaneous CO₂flux measurements. CO₂pulses consistently increased with temperature, and temperature at time of wetting positively correlated to CO₂pulse magnitude. Experimentally adding N along the N deposition gradient generated contrasting pulse responses: adding N increased CO₂pulses in low N deposition sites, whereas adding N decreased CO₂pulses in high N deposition sites. At a low N deposition site, simultaneous additions of C and N during wetting led to the highest observed soil CO₂fluxes reported globally at 299.5 μmol CO₂ m⁻² s⁻¹. Our results suggest that soils have the capacity to emit high amounts of CO₂within small timeframes following infrequent wetting, and pulse sizes reflect a non‐linear combination of soil resource and temperature interactions. Importantly, the largest soil CO₂emissions occurred when multiple resources were amended simultaneously in historically resource‐limited desert soils, pointing to regions experiencing simultaneous effects of desertification and urbanization as key locations in future global C balance. 

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4. The role of soil redox conditions in microbial phosphorus cycling in humid tropical forests

   https://doi.org/10.1002/ecy.2928  

   Gross, Avner; Lin, Yang; Weber, Peter K.; Pett‐Ridge, Jennifer; Silver, Whendee L. (December 2019, Ecology)

   Abstract Humid tropical forests are among the most productive ecosystems globally, yet they often occur on soils with high phosphorus (P) sorption capacity, lowering P availability to biota. Short‐term anoxic events are thought to release sorbed P and enhance its acquisition by soil microbes. However, the actual effects of anoxic conditions on microbial P acquisition in humid tropical forest soils are surprisingly poorly studied. We used laboratory incubations of bulk soils, NanoSIMS analysis of single microbial cells, and landscape‐scale measurements in the Luquillo Experimental Forest (LEF), Puerto Rico to test the hypothesis that anoxic conditions increase microbial P acquisition in humid tropical forests. In laboratory and field experiments, we found that microbial P uptake generally decreased under anoxic conditions, leading to high microbial carbon (C) to P ratios in anoxic soils. The decreased P acquisition under anoxic conditions was correlated with lower microbial C use efficiency (CUE), an index of microbial energy transfer in ecosystems. Phosphorus amendments to anoxic soils led to increased microbial P uptake and higher CUE suggesting that microbes were less able to access and utilize P under natural low redox conditions. Under oxic conditions, microbial C:P ratios and CUE did not respond to changes in substrate stoichiometry. These results challenge the existing paradigm by showing that anoxic conditions can decrease microbial P uptake and ultimately constrain microbial CUE. Our findings indicate that soil redox conditions tightly couple soil P and C cycles and advance our understanding of controls on P cycling in humid tropical forest ecosystems. 

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5. Long‐term nitrogen deposition inhibits soil priming effects by enhancing phosphorus limitation in a subtropical forest

   https://doi.org/10.1111/gcb.16718  

   Wang, Xiaohong; Li, Shiyining; Zhu, Biao; Homyak, Peter M.; Chen, Guangshui; Yao, Xiaodong; Wu, Dongmei; Yang, Zhijie; Lyu, Maokui; Yang, Yusheng (April 2023, Global Change Biology)

   Abstract It is widely accepted that phosphorus (P) limits microbial metabolic processes and thus soil organic carbon (SOC) decomposition in tropical forests. Global change factors like elevated atmospheric nitrogen (N) deposition can enhance P limitation, raising concerns about the fate of SOC. However, how elevated N deposition affects the soil priming effect (PE) (i.e., fresh C inputs induced changes in SOC decomposition) in tropical forests remains unclear. We incubated soils exposed to 9 years of experimental N deposition in a subtropical evergreen broadleaved forest with two types of¹³C‐labeled substrates of contrasting bioavailability (glucose and cellulose) with and without P amendments. We found that N deposition decreased soil total P and microbial biomass P, suggesting enhanced P limitation. In P unamended soils, N deposition significantly inhibited the PE. In contrast, adding P significantly increased the PE under N deposition and by a larger extent for the PE of cellulose (PE_cellu) than the PE of glucose (PE_glu). Relative to adding glucose or cellulose solely, adding P with glucose alleviated the suppression of soil microbial biomass and C‐acquiring enzymes induced by N deposition, whereas adding P with cellulose attenuated the stimulation of acid phosphatase (AP) induced by N deposition. Across treatments, the PE_gluincreased as C‐acquiring enzyme activity increased, whereas the PE_celluincreased as AP activity decreased. This suggests that P limitation, enhanced by N deposition, inhibits the soil PE through varying mechanisms depending on substrate bioavailability; that is, P limitation regulates the PE_gluby affecting soil microbial growth and investment in C acquisition, whereas regulates the PE_celluby affecting microbial investment in P acquisition. These findings provide new insights for tropical forests impacted by N loading, suggesting that expected changes in C quality and P limitation can affect the long‐term regulation of the soil PE. 

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