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1. Bacterial Community Structure Modulates Soil Phosphorus Turnover at Early Stages of Primary Succession

   https://doi.org/10.1029/2024GB008174  

   Wang, Yuhan; Bing, Haijian; Moorhead, Daryl L; Hou, Enqing; Wu, Yanhong; Wang, Jipeng; Duan, Chengjiao; Cui, Qingliang; Zhang, Zhiqin; Zhu, He; et al (October 2024, Global Biogeochemical Cycles)

   Abstract Microbes are the drivers of soil phosphorus (P) cycling in terrestrial ecosystems; however, the role of soil microbes in mediating P cycling in P‐rich soils during primary succession remains uncertain. This study examined the impacts of bacterial community structure (diversity and composition) and its functional potential (absolute abundances of P‐cycling functional genes) on soil P cycling along a 130‐year glacial chronosequence on the eastern Tibetan Plateau. Bacterial community structure was a better predictor of soil P fractions than P‐cycling genes along the chronosequence. After glacier retreat, the solubilization of inorganic P and the mineralization of organic P were significantly enhanced by increased bacterial diversity, changed interspecific interactions, and abundant species involved in soil P mineralization, thereby increasing P availability. Although 84% of P‐cycling genes were associated with organic P mineralization, these genes were more closely associated with soil organic carbon than with organic P. Bacterial carbon demand probably determined soil P turnover, indicating the dominant role of organic matter decomposition processes in P‐rich alpine soils. Moreover, the significant decrease in the complexity of the bacterial co‐occurrence network and the taxa‐gene‐P network at the later stage indicates a declining dominance of the bacterial community in driving soil P cycling with succession. Our results reveal that bacteria with a complex community structure have a prominent potential for biogeochemical P cycling in P‐rich soils during the early stages of primary succession. 

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2. Phosphorus chemistry in plant charcoal: interplay between biomass composition and thermal condition

   https://doi.org/10.1071/WF23096  

   Wu, Yudi; Pae, Lois M; Huang, Rixiang (January 2024, International Journal of Wildland Fire)

   Background Vegetation fire may change Phosphorus (P) cycling in terrestrial ecosystems through converting biomass into fire residues. Aim The aim of this study was to understand the chemistry and mobility of P in fire residues to help reveal P thermochemistry during biomass burning and post-fire P cycling. Methods A combination of sequential extraction, liquid 31P NMR and P K-edge XANES was used to obtain quantitative P speciation and explain P solubilisation behaviours of charcoal. Key results Despite varying diverse P species existing in raw biomass, only two P structural moieties – orthophosphate and pyrophosphate – were identified in charcoal. However, relative abundance of pyrophosphate differs greatly among charcoal samples from different biomass types, ranging between 0 and 40% of total extractable P. Although P K-edge XANES data indicates abundant soluble phosphate minerals, most P (70–90%) is likely occluded physically in the charcoal. The bicarbonate-extractable P (the Olsen-P) varies significantly and cannot be explained by surface P concentration or elemental stoichiometry alone. Conclusion and implications The results suggest the importance of starting biomass P speciation (i.e. molecular structure and complexation environment) and thermal conditions in controlling P speciation and availability in charcoal. The different P chemistry between charcoal and ash suggests the importance of fire types and severity in disturbing the P cycle. 

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3. The eigensplitting of the fiber of the cyclotomic trace for the sphere spectrum

   https://doi.org/10.1090/tran/8822  

   Blumberg, Andrew; Mandell, Michael (January 2022, Transactions of the American Mathematical Society)

   Let p ∈ Z p\in {\mathbb {Z}} be an odd prime. We show that the fiber sequence for the cyclotomic trace of the sphere spectrum S {\mathbb {S}} admits an “eigensplitting” that generalizes known splittings on K K -theory and T C TC . We identify the summands in the fiber as the covers of Z p {\mathbb {Z}}_{p} -Anderson duals of summands in the K ( 1 ) K(1) -localized algebraic K K -theory of Z {\mathbb {Z}} . Analogous results hold for the ring Z {\mathbb {Z}} where we prove that the K ( 1 ) K(1) -localized fiber sequence is self-dual for Z p {\mathbb {Z}}_{p} -Anderson duality, with the duality permuting the summands by i ↦ p − i i\mapsto p-i (indexed mod p − 1 p-1 ). We explain an intrinsic characterization of the summand we call Z Z in the splitting T C ( Z ) p ∧ ≃ j ∨ Σ j ′ ∨ Z TC({\mathbb {Z}})^{\wedge }_{p}\simeq j \vee \Sigma j’\vee Z in terms of units in the p p -cyclotomic tower of Q p {\mathbb {Q}}_{p} . 

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4. High species richness in the lichen genus Peltigera (Ascomycota, Lecanoromycetes): 34 species in the dolichorhizoid and scabrosoid clades of section Polydactylon, including 24 new to science

   https://doi.org/10.3767/persoonia.2023.51.01  

   Magain, N.; Miadlikowska, J.; Goffinet, B.; Goward, T.; Pardo-De la Hoz, C.J.; Jüriado, I.; Simon, A.; Mercado-Díaz, J.A.; Barlow, T.; Moncada, B.; et al (August 2023, Persoonia - Molecular Phylogeny and Evolution of Fungi)

   Applying molecular methods to fungi establishing lichenized associations with green algae or cyanobacteria has repeatedly revealed the existence of numerous phylogenetic taxa overlooked by classical taxonomic approaches. Here, we report taxonomical conclusions based on multiple species delimitation and validation analyses performed on an eight-locus dataset that includes world-wide representatives of the dolichorhizoid and scabrosoid clades in section Polydactylon of the genus Peltigera . Following the recommendations resulting from a consensus species delimitation approach and additional species validation analysis (BPP) performed in this study, we present a total of 25 species in the dolichorhizoid clade and nine in the scabrosoid clade, including respectively 18 and six species that are new to science and formally described. Additionally, one combination and three varieties (including two new to science) are proposed in the dolichorhizoid clade. The following 24 new species are described: P. appalachiensis , P. asiatica , P. borealis , P. borinquensis , P. chabanenkoae , P. clathrata , P. elixii , P. esslingeri , P. flabellae , P. gallowayi , P. hawaiiensis , P. holtanhartwigii , P. itatiaiae , P. hokkaidoensis , P. kukwae , P. massonii , P. mikado , P. nigriventris , P. orientalis , P. rangiferina , P. sipmanii , P. stanleyensis , P. vitikainenii and P. willdenowii ; the following new varieties are introduced: P. kukwae var. phyllidiata and P. truculenta var. austroscabrosa ; and the following new combination is introduced: P. hymenina var. dissecta . Each species from the dolichorhizoid and scabrosoid clades is morphologically and chemically described, illustrated, and characterised with ITS sequences. Identification keys are provided for the main biogeographic regions where species from the two clades occur. Morphological and chemical characters that are commonly used for species identification in the genus Peltigera cannot be applied to unambiguously recognise most molecularly circumscribed species, due to high variation of thalli formed by individuals within a fungal species, including the presence of distinct morphs in some cases, or low interspecific variation in others. The four commonly recognised morphospecies: P. dolichorhiza , P. neopolydactyla , P. pulverulenta and P. scabrosa in the dolichorhizoid and scabrosoid clades represent species complexes spread across multiple and often phylogenetically distantly related lineages. Geographic origin of specimens is often helpful for species recognition; however, ITS sequences are frequently required for a reliable identification. 

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5. Automatically Reproducing Timing-Dependent Flaky-Test Failures

   https://doi.org/10.5281/zenodo.7041599  

   Shanto Rahman, Aaron Massey (January 2023, Zenodo)

   This artifact contains the source code for FlakeRake, a tool for automatically reproducing timing-dependent flaky-test failures. It also includes raw and processed results produced in the evaluation of FlakeRake   Contents:   Timing-related APIs that FlakeRake considers adding sleeps at: timing-related-apis Anonymized code for FlakeRake (not runnable in its anonymized state, but included for reference; we will publicly release the non-anonymized code under an open source license pending double-blind review): flakerake.tgz Failure messages extracted from the FlakeFlagger dataset: 10k_reruns_failures_by_test.csv.gz  Output from running isolated reruns on each flaky test in the FlakeFlager dataset: 10k_isolated_reruns_all_results.csv.gz (all test results summarized into a CSV), 10k_isolated_reruns_failures_by_test.csv.gz (CSV including just test failures, including failure messages), 10k_isolated_reruns_raw_results.tgz (includes all raw results from reruns, including the XML files output by maven) Output from running the FlakeFlagger replication study (non-isolated 10k reruns):flakeFlaggerReplResults.csv.gz (all test results summarized into a CSV), 10k_reruns_failures_by_test.csv.gz (CSV including just failures, including failure messages), flakeFlaggerRepl_raw_results.tgz (includes all raw results from reruns, including the XML files output by maven - this file is markedly larger than the 10k isolated reruns results because we ran *all* tests in this experiment, whereas the 10k isolated rerun experiment only re-ran the tests that were known to be flaky from the FlakeFlagger dataset). Output from running FlakeRake on each flaky test in the FlakeFlagger dataset: For bisection mode: results-bis.tgz For one-by-one mode: results-obo.tgz Scripts used to execute FlakeRake using an HPC cluster: execution-scripts.tgz Scripts used to execute rerun experiments using an HPC cluster: flakeFlaggerReplScripts.tgz Scripts used to parse the "raw" maven test result XML files in this artifact into the CSV files contained in this artifact: parseSurefireXMLs.tgz  Output from running FlakeRake in “reproduction” mode, attempting to reproduce each of the failures that matched the FlakeFlagger dataset (collected for bisection mode only): results-repro-bis.tgz Analysis of timing-dependent API calls in the failure inducing configurations that matched FlakeFlagger failures: bis-sleepyline.cause-to-matched-fail-configs-found.csv 

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