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1. Defining the Sphagnum Core Microbiome across the North American Continent Reveals a Central Role for Diazotrophic Methanotrophs in the Nitrogen and Carbon Cycles of Boreal Peatland Ecosystems

   https://doi.org/10.1128/mbio.03714-21  

   Kolton, Max ; Weston, David J. ; Mayali, Xavier ; Weber, Peter K. ; McFarlane, Karis J. ; Pett-Ridge, Jennifer ; Somoza, Mark M. ; Lietard, Jory ; Glass, Jennifer B. ; Lilleskov, Erik A. ; et al ( February 2022 , mBio)

   Martiny, Jennifer B. (Ed.)

   ABSTRACT Peat mosses of the genus Sphagnum are ecosystem engineers that frequently predominate over photosynthetic production in boreal peatlands. Sphagnum spp. host diverse microbial communities capable of nitrogen fixation (diazotrophy) and methane oxidation (methanotrophy), thereby potentially supporting plant growth under severely nutrient-limited conditions. Moreover, diazotrophic methanotrophs represent a possible “missing link” between the carbon and nitrogen cycles, but the functional contributions of the Sphagnum -associated microbiome remain in question. A combination of metagenomics, metatranscriptomics, and dual-isotope incorporation assays was applied to investigate Sphagnum microbiome community composition across the North American continent and provide empirical evidence for diazotrophic methanotrophy in Sphagnum -dominated ecosystems. Remarkably consistent prokaryotic communities were detected in over 250 Sphagnum SSU rRNA libraries from peatlands across the United States (5 states, 17 bog/fen sites, 18 Sphagnum species), with 12 genera of the core microbiome comprising 60% of the relative microbial abundance. Additionally, nitrogenase ( nifH ) and SSU rRNA gene amplicon analysis revealed that nitrogen-fixing populations made up nearly 15% of the prokaryotic communities, predominated by Nostocales cyanobacteria and Rhizobiales methanotrophs. While cyanobacteria comprised the vast majority (>95%) of diazotrophs detected in amplicon and metagenome analyses, obligate methanotrophs of the genus Methyloferula (order Rhizobiales ) accounted for one-quarter of transcribed nifH genes. Furthermore, in dual-isotope tracer experiments, members of the Rhizobiales showed substantial incorporation of 13 CH 4 and 15 N 2 isotopes into their rRNA. Our study characterizes the core Sphagnum microbiome across large spatial scales and indicates that diazotrophic methanotrophs, here defined as obligate methanotrophs of the rare biosphere ( Methyloferula spp. of the Rhizobiales ) that also carry out diazotrophy, play a keystone role in coupling of the carbon and nitrogen cycles in nutrient-poor peatlands. IMPORTANCE Nitrogen availability frequently limits photosynthetic production in Sphagnum moss-dominated high-latitude peatlands, which are crucial carbon-sequestering ecosystems at risk to climate change effects. It has been previously suggested that microbial methane-fueled fixation of atmospheric nitrogen (N 2 ) may occur in these ecosystems, but this process and the organisms involved are largely uncharacterized. A combination of omics (DNA and RNA characterization) and dual-isotope incorporation approaches illuminated the functional diversity of Sphagnum -associated microbiomes and defined 12 bacterial genera in its core microbiome at the continental scale. Moreover, obligate diazotrophic methanotrophs showed high nitrogen fixation gene expression levels and incorporated a substantial amount of atmospheric nitrogen and methane-driven carbon into their biomass. Thus, these results point to a central role for members of the rare biosphere in Sphagnum microbiomes as keystone species that couple nitrogen fixation to methane oxidation in nutrient-poor peatlands. 

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2. Light-induced psbA translation in plants is triggered by photosystem II damage via an assembly-linked autoregulatory circuit

   https://doi.org/10.1073/pnas.2007833117  

   Chotewutmontri, Prakitchai ; Barkan, Alice ( August 2020 , Proceedings of the National Academy of Sciences)

   The D1 reaction center protein of photosystem II (PSII) is subject to light-induced damage. Degradation of damaged D1 and its replacement by nascent D1 are at the heart of a PSII repair cycle, without which photosynthesis is inhibited. In mature plant chloroplasts, light stimulates the recruitment of ribosomes specifically topsbAmRNA to provide nascent D1 for PSII repair and also triggers a global increase in translation elongation rate. The light-induced signals that initiate these responses are unclear. We present action spectrum and genetic data indicating that the light-induced recruitment of ribosomes topsbAmRNA is triggered by D1 photodamage, whereas the global stimulation of translation elongation is triggered by photosynthetic electron transport. Furthermore, mutants lacking HCF136, which mediates an early step in D1 assembly, exhibit constitutively highpsbAribosome occupancy in the dark and differ in this way from mutants lacking PSII for other reasons. These results, together with the recent elucidation of a thylakoid membrane complex that functions in PSII assembly, PSII repair, andpsbAtranslation, suggest an autoregulatory mechanism in which the light-induced degradation of D1 relieves repressive interactions between D1 and translational activators in the complex. We suggest that the presence of D1 in this complex coordinates D1 synthesis with the need for nascent D1 during both PSII biogenesis and PSII repair in plant chloroplasts.

    

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3. Soil nitrogen fertilization reduces relative leaf nitrogen allocation to photosynthesis

   https://doi.org/10.1093/jxb/erad195  

   Waring, Elizabeth F. ; Perkowski, Evan A. ; Smith, Nicholas G. ; Rogers, ed., Alistair ( May 2023 , Journal of Experimental Botany)

   The connection between soil nitrogen availability, leaf nitrogen, and photosynthetic capacity is not perfectly understood. Because these three components tend to be positively related over large spatial scales, some posit that soil nitrogen positively drives leaf nitrogen, which positively drives photosynthetic capacity. Alternatively, others posit that photosynthetic capacity is primarily driven by above-ground conditions. Here, we examined the physiological responses of a non-nitrogen-fixing plant (Gossypium hirsutum) and a nitrogen-fixing plant (Glycine max) in a fully factorial combination of light by soil nitrogen availability to help reconcile these competing hypotheses. Soil nitrogen stimulated leaf nitrogen in both species, but the relative proportion of leaf nitrogen used for photosynthetic processes was reduced under elevated soil nitrogen in all light availability treatments due to greater increases in leaf nitrogen content than chlorophyll and leaf biochemical process rates. Leaf nitrogen content and biochemical process rates in G. hirsutum were more responsive to changes in soil nitrogen than those in G. max, probably due to strong G. max investments in root nodulation under low soil nitrogen. Nonetheless, whole-plant growth was significantly enhanced by increased soil nitrogen in both species. Light availability consistently increased relative leaf nitrogen allocation to leaf photosynthesis and whole-plant growth, a pattern that was similar between species. These results suggest that the leaf nitrogen–photosynthesis relationship varies under different soil nitrogen levels and that these species preferentially allocated more nitrogen to plant growth and non-photosynthetic leaf processes, rather than photosynthesis, as soil nitrogen increased.

    

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4. Leaf nitrogen affects photosynthesis and water use efficiency similarly in nitrogen‐fixing and non‐fixing trees

   https://doi.org/10.1111/1365-2745.14194  

   Bytnerowicz, Thomas A. ; Funk, Jennifer L. ; Menge, Duncan N. L. ; Perakis, Steven S. ; Wolf, Amelia A. ( September 2023 , Journal of Ecology)

   Nitrogen (N)‐fixing trees are thought to break a basic rule of leaf economics: higher leaf N concentrations do not translate into higher rates of carbon assimilation. Understanding how leaf N affects photosynthesis and water use efficiency (WUE) in this ecologically important group is critical.

   We grew six N‐fixing and four non‐fixing tree species for 4–5 years at four fertilization treatments in field experiments in temperate and tropical regions to assess how functional type (N fixer vs. non‐fixer) and N limitation affected leaf N and how leaf N affected light‐saturated photosynthesis (A_sat), stomatal conductance (g_sw) and WUE (WUE_iand δ¹³C).

   A_sat, WUE_iand δ¹³C, but notg_sw, increased with higher leaf N. Surprisingly, N‐fixing and non‐fixing trees displayed similar scaling between leaf N and these physiological variables, and this finding was supported by reanalysis of a global dataset. N fixers generally had higher leaf N than non‐fixers, even when non‐fixers were not N‐limited at the leaf level. Leaf‐level N limitation did not alter the relationship ofA_sat,g_sw, WUE_iand δ¹³C with leaf N, although it did affect the photosynthetic N use efficiency. Higher WUE was associated with higher productivity, whereas higherA_satwas not.

   Synthesis: The ecological success of N‐fixing trees depends on the effect of leaf N on carbon gain and water loss. Using a field fertilization experiment and reanalysis of a global dataset, we show that high leaf‐level photosynthesis and WUE in N fixers stems from their higher average leaf N, rather than a difference between N fixers and non‐fixers in the scaling of photosynthesis and WUE with leaf N. By clarifying the mechanism by which N fixers achieve and benefit from high WUE, our results further the understanding of global N fixer distributions.

    

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5. Plasticity of Arabidopsis rosette transcriptomes and photosynthetic responses in dynamic light conditions

   https://doi.org/10.1002/pld3.475  

   Alameldin, Hussien F. ; Montgomery, Beronda L. ( January 2023 , Plant Direct)

   With the high variability of natural growth environments, plants exhibit flexibility and resilience in regard to the strategies they employ to maintain overall fitness, including maximizing light use for photosynthesis, while simultaneously limiting light‐associated damage. We measured distinct parameters of photosynthetic performance ofArabidopsis thalianaplants under dynamic light regimes. Plants were grown to maturity then subjected to the following 5‐day (16 h light, 8 h dark) regime: Day 1 at constant light (CL) intensity during light period, representative of a common lab growth condition; Day 2 under sinusoidal variation in light intensity (SL) during the light period that is representative of changes occurring during a clear sunny day; Day 3 under fluctuating light (FL) intensity during the light period that simulates sudden changes that might occur with the movements of clouds in and out of the view of the sun; Day 4, repeat of CL; and Day 5, repeat of FL. We also examined the global transcriptome profile in these growth conditions based on obtaining RNA‐sequencing (RNA‐seq) data for whole plant rosettes. Our transcriptomic analyses indicated downregulation of photosystem I (PSI) and II (PSII) associated genes, which were correlated with elevated levels of photoinhibition as indicated by measurements of nonphotochemical quenching (NPQ), energy‐dependent quenching (q_E), and inhibitory quenching (q_I) under both SL and FL conditions. Furthermore, our transcriptomic results indicated downregulation of tetrapyrrole biosynthesis associated genes, coupled with reduced levels of chlorophyll under both SL and FL compared with CL, as well as downregulation of photorespiration‐associated genes under SL. We also noticed an enrichment of the stress response gene ontology (GO) terms for genes differentially regulated under FL when compared with SL. Collectively, our phenotypic and transcriptome analyses serve as useful resources for probing the underlying molecular mechanisms associated with plant acclimation to rapid light intensity changes in the natural environment.

    

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