Of sea, rivers and symbiosis: Diversity, systematics, biogeography and evolution of the deeply diverging florideophycean order Hildenbrandiales (Rhodophyta).

The Hildenbrandiales, a typically saxicolous red algal order, is an early diverging florideophycean group with global significance in marine and freshwater ecosystems across diverse temperature zones. To comprehensively elucidate the diversity, phylogeny, biogeography, and evolution of this order, we conducted a thorough re-examination employing molecular data derived from nearly 700 specimens. Employing a species delimitation method, we identified Evolutionary Species Units (ESUs) within the Hildenbrandiales aiming to enhance our understanding of species diversity and generate the first time-calibrated tree and ancestral area reconstruction for this order. Mitochondrial cox1 and chloroplast rbcL markers were used to infer species boundaries, and subsequent phylogenetic reconstructions involved concatenated sequences of cox1, rbcL, and 18S rDNA. Time calibration of the resulting phylogenetic tree used a fossil record from a Triassic purportedly freshwater Hildenbrandia species and three secondary time points from the literature. Our species delimitation analysis revealed an astounding 97 distinct ESUs, quintupling the known diversity within this order. Our time-calibration analysis placed the origin of Hildenbrandiales (crown age) in the Ediacaran period, with freshwater species emerging as a monophyletic group during the later Permian to early Triassic. Phylogenetic reconstructions identified seven major clades, experiencing early diversification during the Silurian to Carboniferous period. Two major evolutionary events-colonization of freshwater habitats and obligate systemic symbiosis with a marine fungus-marked this order, leading to significant morphological alterations without a commensurate increase in species diversification. Despite the remarkable newly discovered diversity, the extant taxon diversity appears relatively constrained when viewed against an evolutionary timeline spanning over 800 million years. This limitation may stem from restricted geographic sampling or the prevalence of asexual reproduction. However, species richness estimation and rarefaction analyses suggest a substantially larger diversity yet to be uncovered-potentially four times greater. These findings drastically reshape our understanding of the deeply diverging florideophycean order Hildenbrandiales species diversity, and contribute valuable insights into this order's evolutionary history and ecological adaptations. Supported by phylogenetic, ecological and morphological evidence, we established the genus Riverina gen. nov. to accommodate freshwater species of Hildenbrandiales, which form a monophyletic clade in our analyses. This marks the first step toward refining the taxonomy of the Hildenbrandiales, an order demanding thorough revisions, notably with the creation of several genera to address the polyphyletic status of Hildenbrandia. However, the limited diagnostic features pose a challenge, necessitating a fresh approach to defining genera. A potential solution lies in embracing a molecular systematic perspective, which can offer precise delineations of taxonomic boundaries.

French Polynesian Scytosiphonaceae (Ectocarpales, Phaeophyceae): A combined molecular and morphological approach to their diversity and systematics.

This study revisited the taxonomy and diversity of brown macroalgae within the Scytosiphonaceae family in French Polynesia, which had previously been recognized as encompassing only six species. Using the chloroplast and mitochondrial genes rbcL, psbA, and cox3 as molecular markers in conjunction with morpho-anatomical observations, we unveiled the presence of 11 species spanning six genera: Chnoospora minima, Colpomenia claytoniae, Co. sinuosa [groups IIIa and IIIb], Hydroclathrus rapanuii, H. tenuis, H. tilesii, Manzaea minuta, Pseudochnoospora implexa, Rosenvingea australis, and the newly described species R. polynesiensis sp. nov. and R. tahitiensis sp. nov. This encompasses the recognition of two previously unreported genera in this region: Manzaea and Pseudochnoospora. Sequences were successfully acquired for four taxa that had been documented previously, while the absence of sequences for H. clathratus and H. tumulis in French Polynesia raises queries about their presence in this region. With these additions, the total species count now stands at 13 (including H. clathratus and H. tumulis), one being an endemic species. The molecular-assisted alpha taxonomic approach used here allowed for a critical revision of the Scytosiphonaceae species checklist for French Polynesia. The diversity revealed in this region accounts for a substantial 20% of the family's global diversity. Additionally, our study presents an updated species-level phylogeny for the Scytosiphonaceae.

Marine Flora of French Polynesia: An Updated List Using DNA Barcoding and Traditional Approaches.

Located in the heart of the South Pacific Ocean, the French Polynesian islands represent a remarkable setting for biological colonization and diversification, because of their isolation. Our knowledge of this region's biodiversity is nevertheless still incomplete for many groups of organisms. In the late 1990s and 2000s, a series of publications provided the first checklists of French Polynesian marine algae, including the Chlorophyta, Rhodophyta, Ochrophyta, and Cyanobacteria, established mostly on traditional morphology-based taxonomy. We initiated a project to systematically DNA barcode the marine flora of French Polynesia. Based on a large collection of ~2452 specimens, made between 2014 and 2023, across the five French Polynesian archipelagos, we re-assessed the marine floral species diversity (Alismatales, Cyanobacteria, Rhodophyta, Ochrophyta, Chlorophyta) using DNA barcoding in concert with morphology-based classification. We provide here a major revision of French Polynesian marine flora, with an updated listing of 702 species including 119 Chlorophyta, 169 Cyanobacteria, 92 Ochrophyta, 320 Rhodophyta, and 2 seagrass species-nearly a two-fold increase from previous estimates. This study significantly improves our knowledge of French Polynesian marine diversity and provides a valuable DNA barcode reference library for identification purposes and future taxonomic and conservation studies. A significant part of the diversity uncovered from French Polynesia corresponds to unidentified lineages, which will require careful future taxonomic investigation.

Marine Floral Biodiversity, Threats, and Conservation in Vietnam: An Updated Review.

Part of the Indo-Chinese peninsula and located on the northwest edge of the Coral Triangle in the South China Sea, the Vietnamese coastal zone is home to a wealthy marine biodiversity associated with the regional geological setting and history, which supports a large number of marine ecosystems along a subtropical to tropical gradient. The diversity of coastal benthic marine primary producers is also a key biological factor supporting marine biological diversity. The present review provides: (1) an updated checklist of the Vietnamese marine flora, (2) a review of molecular-assisted alpha taxonomic efforts, (3) an analysis of marine floral biodiversity spatial distribution nationally and regionally (South China Sea), (4) a review of the impact of anthropogenic and environmental stressors on the Vietnamese marine flora, and (5) the efforts developed in the last decade for its conservation. Based on the studies conducted since 2013 and the nomenclatural changes that occurred during this period, an updated checklist of benthic marine algae and seagrasses consisted in a new total of 878 species, including 439 Rhodophyta, 156 Ochrophyta, 196 Chlorophyta, 87 Cyanobacteria, and 15 phanerogam seagrasses. This update contains 54 new records and 5 new species of macroalgae. The fairly poor number of new records and new species identified in the last 10 years in a "mega-diverse" country can be largely attributed to the limited efforts in exploring algal biodiversity and the limited use of genetic tools, with only 25.4% (15 species) of these new records and species made based on molecular-assisted alpha taxonomy. The South Central Coast supports the highest species diversity of marine algae, which coincides with the largest density of coral reefs along the Vietnamese coast. Vietnam holds in the South China Sea one of the richest marine floras, imputable to the country's geographical, geological, and climatic settings. However, Vietnam marine floral biodiversity is under critical threats examined here, and current efforts are insufficient for its conservation. A methodical molecular-assisted re-examination of Vietnam marine floral biodiversity is urgently needed, complemented with in-depth investigations of the main threats targeting marine flora and vulnerable taxa, and finally, conservation measures should be urgently implemented.

Diversity and Ecology of Lobophora Species Associated with Coral Reef Systems in the Western Gulf of Thailand, including the Description of Two New Species.

The brown macroalgal genus Lobophora plays important ecological roles in many marine ecosystems. This group has received much attention over the past decade, and a considerable number of new species have been identified globally. However, our knowledge of the genus diversity and ecology along south-east Asian coasts are still limited. Given the growing body of research that uses a combination of molecular and morphological data to identify cryptic species, this study investigates the diversity of Lobophora in the western Gulf of Thailand using morphological and molecular data, as well as their interactions with scleractinian corals. A total of 36 Lobophora specimens were collected from 15 sites in the western Gulf of Thailand and used for molecular and morphological analyses. One mitochondrial (cox3) and two chloroplast (psbA and rbcL) genes were amplified and sequenced for molecular phylogenetic analyses. Based primarily on phylogenetic evidence, two new species were formally described, L. chumphonensis sp. nov. and L. thailandensis sp. nov. Additionally, L. lamourouxii was newly recorded from Thailand. Two new lineages of Lobophora obscura were identified, L. obscura12 and L. obscura13. Among the Lobophora species identified, three were found in interaction with corals, the most notable of which was the massive coral Porites. Lobophora chumphonensis sp. nov. only interacted with Porites by growing on bare coral skeleton between Porites colonies. Furthermore, L. obscura13 was observed under the branching coral Pocillopora. Our findings revealed that Lobophora presented both effects and absence of effects on coral. A thorough understanding of Lobophora diversity and ecology is essential for ongoing and future research on coral-macroalgal ecological relationships.

Taxonomic Revision of Hook-Forming Acrosorium (Delesseriaceae, Rhodophyta) from the Northwestern Pacific Based on Morphology and Molecular Data.

Cosmopolitan Acrosorium species with hook-forming thalli have been merged under the name of Acrosorium ciliolatum (Harvey) Kylin through a long and complicated nomenclatural history. We examined the specimens of 'A. ciliolatum' and related taxa from the northwestern (NW) Pacific, the UK, southern Spain, Australia, New Zealand, and Chile, using morphological and molecular analyses. We confirmed that these specimens are separated into four clades based on rbcL phylogeny, and the absence or presence of terminal hook-like structures represent intraspecific variation. Our results indicated that Acrosorium flabellatum Yamada, Cryptopleura hayamensis Yamada, Cryptopleura membranacea Yamada and the entities known as 'A. ciliolatum' in the NW Pacific are conspecific; the name A. flabellatum is the oldest and has priority. This taxon exhibits extreme variations in external blade morphology. We also confirmed that the position of the tetrasporangial sori is a valuable diagnostic characteristic for distinguishing A. flabellatum in the NW Pacific. We also discussed the need for further study of European and southern hemisphere specimens from type localities, as well as the ambiguous position of California specimens.

Verification of hotspots of genetic diversity in Korean population of Grateloupia asiatica and G. jejuensis (Rhodophyta) show low genetic diversity and similar geographic distribution.

BACKGROUND: Understanding the genetic diversity and distribution patterns of seaweeds species is crucial for evaluating key regions of high genetic diversity. Identifying hotspots of high intraspecific diversity is an important step for developing conservation strategies. Grateloupia is a diverse genus of Rhodophyta, many of which are resource of numerous useful bioactive compounds; therefore, the genus is valuable target for conservation. OBJECTIVE: The aim of this study is to examine the genetic diversity and population structure of two Grateloupia species, Grateloupia asiatica and Grateloupia jejuensis, with the understanding of the phylogeography of the Korean genetic diversity hotspot for two species. METHODS: Plastid rbcL gene sequences of 134 specimens of G. asiatica and 112 specimens of G. jejuensis collected from the Korean coast were analyzed. We evaluated the number of haplotypes, genetic diversity (haplotype and nucleotide diversity), and haplotype networks of two species. Historical demographic was inferred by calculating neutrality tests and genetic differentiation was estimated using the fixation index, FST. RESULTS: Our results show that both species are generally similar in geographical distribution patterns, that is, relatively homogeneous with few haplotypes derived from the most frequent haplotype. The east coast of Korea is identified as a 'hotspot' with the highest genetic diversity for both species, whereas Jeju Island is identified as a 'cold spot' with the lowest genetic diversity for G. jejuensis. Analyses across most distribution ranges of the two species in Korea reveal low genetic and haplotype diversities, which could indicate that these two Grateloupia species have either experienced a historical lack of diversity or a recent reduction in diversity due to high gene flow. CONCLUSIONS: The low genetic diversity values found in the present study raise considerable concern about the conservation status of these two Grateloupia species and highlight the need to locate further hotspots of genetic diversity to strengthen their resilience against further decline.

Foliar-Applied Glutathione Mitigates Cadmium-Induced Oxidative Stress by Modulating Antioxidant-Scavenging, Redox-Regulating, and Hormone-Balancing Systems in Brassica napus.

The antioxidant glutathione (GSH) mitigates adverse physio-metabolic effects and defends against abiotic types of stress, such as cadmium (Cd) stress. However, its function and role in resisting Cd phytotoxicity by leveraging plant antioxidant-scavenging, redox-regulating, and hormone-balancing systems have not been comprehensively and systematically demonstrated in the Cd-hyperaccumulating plant Brassica napus L. cv. Tammi (oilseed rape). In this study, the effects of exogenously applied GSH to the leaves of B. napus seedlings exposed to Cd (10 µM) were investigated. As a result, Cd stress alone significantly inhibited growth and increased the levels of reactive oxygen species (ROS) and the bioaccumulation of Cd in the seedlings compared with those in unstressed controls. Furthermore, Cd stress induced an imbalance in plant stress hormone levels and decreases in endogenous GSH levels and GSH redox ratios, which were correlated with reductions in ascorbate (AsA) and/or nicotinamide adenine dinucleotide phosphate (NADPH) redox states. However, the exogenous application of GSH to Cd-stressed B. napus seedlings reduced Cd-induced ROS levels and enhanced antioxidant-scavenging defenses and redox regulation by both increasing seedling AsA, GSH, and NADPH concentrations and rebalancing stress hormones, thereby enhancing Cd uptake and accumulation. These results demonstrate that GSH improved plant redox status by upregulating the AsA-GSH-NADPH cycle and reestablishing normal hormonal balance. This indicates that exogenously applied GSH can mitigate Cd phytotoxicity in B. napus and possibly other plants. Therefore, GSH can potentially be applied to Cd-polluted soil for plant remediation.

Complete mitochondrial genome of Polyopes lancifolius and comparison with related species in Halymeniales (Rhodophyta).

Polyopes lancifolius is a species of Halymeniales, the fifth species-rich order within Rhodophyta. Using next-generation sequencing techniques, we recovered the complete mitochondrial genome of P. lancifolius, i.e. total 26,142 bp in length with 31% GC contents. A total of 49 functional genes were annotated, including 24 protein-coding, 23 transfer RNA, and 2 ribosomal RNA genes. The gene content and synteny have been highly congruent to those of the other halymenialean species, such as Grateloupia taiwanensis, G. filicina, and Grateloupia angusta. Interestingly, the cox1 intron and intronic Open Reading Frame (ORF) are absent in P. lancifolius, that are existed in the other three halymenialean species.

The impact of the Xpert MTB/RIF screening among hospitalized patients with pneumonia on timely isolation of patients with pulmonary tuberculosis.

In South Korea where the tuberculosis (TB) burden is intermediate, the risk of in-hospital transmission of TB remains high. We conducted a retrospective cohort study of 244 inpatients diagnosed with pulmonary TB (2015-2018) to evaluate the impact of the Xpert MTB/RIF assay (Xpert) screening on timely isolation. TB screening was performed with smear microscopy and a polymerase chain reaction test, and the Xpert was additionally used from November 2016. Among all patients with pulmonary TB, the median time-to-isolation was significantly reduced (22.6 vs. 69.7 h; p < 0.001) and segmented regression analysis adjusting for the time trend showed a reduction in time-to-isolation with the introduction of the Xpert (- 39.3 h; 95% CI - 85.6, 7.0; p = 0.096). Among 213 patients who were timely screened (≤ 72 h after admission), time-to-isolation decreased significantly (- 38.2 h; 95% CI - 70.6, - 5.8; p = 0.021) with the introduction of the Xpert, and its decreasing trend continued. The Xpert provided a shorter turnaround time (4.8 vs. 49.1 h; p < 0.001) and higher sensitivity (76.6% vs. 47.8%; p < 0.001) than smear microscopy. Thus, the Xpert can be a useful screening test for pulmonary TB in real-life hospital settings with an intermediate TB burden.

Development and Effect of a Salutogenic Program for Rural Elderly Women on Depression and Suicidal Ideation.

This study aimed to develop and evaluate the effects of a Salutogenic program on sense of coherence, depression, and suicidal ideation among rural older adults. Quasi-experimental, nonequivalent control group pretest-posttest design was used. Participants were female, aged 65 years and older from G and O province, South Korea. The experimental group (n = 22) received a 12-session Salutogenic program for 6 weeks, twice a week. The control group (n = 19) was put on a waiting list to receive the intervention after completing the study. Collected data were analyzed using descriptive statistics, a χ2 test, independent t-test, and repeated measure ANOVA with SPSS WIN 26.0. There were significant differences in sense of coherence (F = 19.34, p < .001), depression (F = 12.93, p < .001), and suicidal ideation (F = 4.40, p = .027) over time pretest, posttest, and follow-up test after intervention between two groups. The study discussed the effect of Salutogenic program on sense of coherence, depression, and suicidal ideation, and considered its benefits in suicide prevention for elderly women. The Salutogenic program can be recommended as useful strategies to enhance sense of coherence and to reduce depression and suicidal ideation of elderly women in community.

Ascorbate-Mediated Modulation of Cadmium Stress Responses: Reactive Oxygen Species and Redox Status in Brassica napus.

The role of ascorbate (AsA) in antioxidant defense system-associated resistance to cadmium (Cd) in oilseed rape plants has not yet been clearly demonstrated. The present study investigated the critical role of exogenous AsA on the physiological and biochemical responses of reactive oxygen species (ROS) and antioxidant scavenging defense systems in oilseed rape (Brassica napus L. cv. Tammi) seedlings exposed to Cd. Cd (10 µM) treatment led to significant reductions in plant growth; increases in the levels of superoxide anion radical, hydrogen peroxide, and malondialdehyde; and increases in Cd uptake and accumulation by the roots and shoots in hydroponically grown 10-day-old seedlings. Moreover, it reduced AsA content and AsA redox ratios, which have been correlated with reductions in glutathione (GSH) and/or nicotinamide adenine dinucleotide phosphate (NADPH) redox status. However, exogenously applying AsA to Cd-exposed seedlings decreased Cd-induced ROS, improved antioxidant defense systems by increasing AsA, GSH, and NADPH contents, and increased Cd uptake and accumulation in both roots and shoots of the plants. These results provided evidence that the enhancement in AsA redox status can be linked to an increase in the GSH and/or NADPH redox ratios through the induction of the AsA-GSH-NADPH cycle. Thus, these results suggest that exogenous AsA application to oilseed rape seedlings under Cd stress might alleviate the overall Cd toxicity by regulating the homeostasis of the AsA-GSH-NADPH cycle, which reestablishes the steady-state cellular redox status.

Flumequine-Mediated Upregulation of p38 MAPK and JNK Results in Melanogenesis in B16F10 Cells and Zebrafish Larvae.

Flumequine is a well-known second generation quinolone antibiotic that induces phototoxicity. However, the effect of flumequine on skin melanogenesis is unclear. Therefore, we, for the first time, investigated whether flumequine regulates melanogenesis. The present study showed that flumequine slightly inhibited in vitro mushroom tyrosinase activity but significantly increased extracellular and intracellular melanin content in B16F10 cells and promoted the expression of microphthalmia-associated transcription factor (MITF) and tyrosinase. Additionally, flumequine remarkably increased melanin pigmentation in zebrafish larvae without any toxicity. We also found that flumequine stimulated p38 mitogen-activated protein kinase (MAPK) and c-Jun N-terminal kinase (JNK) phosphorylation; inhibition of p38 MAPK and JNK resulted in significant downregulation of extracellular and intracellular melanin content in B16F10 cells and pigmentation of zebrafish larvae accompanied with suppression of MITF and tyrosinase expression, indicating that flumequine-mediated p38 and JNK promote melanogenesis in vitro and in vivo. According to the molecular docking prediction, flumequine targeted dual-specificity MAPK phosphatase 16 (DUSP16), which is a major negative regulator of p38 MAPK and JNK. Our findings demonstrate that flumequine induces an increase in melanin content in B16F10 cells and zebrafish larvae by activating p38 MAPK and JNK. These data show the potential of flumequine for use as an anti-vitiligo agent.

Differential modulation of immune response and cytokine profiles of Sargassum horneri ethanol extract in murine spleen with or without Concanavalin A stimulation.

The health benefit of brown seaweeds has been proclaimed for centuries, particularly in Asian countries. A brown seaweed Sargassum horneri has been suggested to have immune-boosting and anti-inflammatory/immune-regulatory effects, but their mechanism is still elusive. This study researches the immunological effect of 70% ethanol extract of S. horneri (SHE) on unstimulated and Con A-stimulated murine splenocytes. When treated alone, SHE had an immune stimulatory effect on CD3e+ CD4+ T-helper cells, CD3e+ CD8+ cytotoxic T cells, CD45+ CD11b+ macrophages, Ly-6C+ Ly-6 G+ granulocytes, and Ly6 G- Ly6Clow eosinophils. Furthermore, SHE enhanced wide spectrum of Th cytokines such as TNF-α, IFN-γ (Th1), IL-4, IL-5, IL-13 (Th2), and IL-6 (Th17), which also stimulated the macrophage polarizing cytokines and enhanced macrophage derived cytokine secretion. SHE in Con A (5 µg/mL) stimulated cells decreased T-helper, cytotoxic T cells, granulocytes, eosinophils, and monocytes. These results signify the potential immuno-modulatory effect of SHE which can be developed as a therapeutic agent in immuno-compromised individuals.

Molecular drug resistance profiles of Mycobacterium tuberculosis from sputum specimens using ion semiconductor sequencing.

The increasing burden of multidrug resistant (MDR)-TB, defined by resistance to rifampin (RFP) and isoniazid (INH), and extensively drug resistant-TB, defined by MDR-TB with additional resistance to fluoroquinolones (FQs) and more than one second-line injectable drug, is a serious impediment to global TB control. We evaluated the feasibility of full-length gene analysis including inhA, katG, rpoB, pncA, rpsL embB, eis, and gyrA using a semiconductor NGS with the Ion AmpliSeq TB panel to directly analyse 34 sputum specimens confirmed by phenotypic DST: INH, RFP, ethambutol (EMB), pyrazinamide (PZA), amikacin, kanamycin, streptomycin (SM), FQs including ofloxacin, moxifloxacin, and levofloxacin. The molecular drug resistance profiles showed "very good" and "substantial" strength of agreement for the phenotypic DST results of RFP and EMB, PZA, SM, FQs resistance with specificities of 96%, and 88%, 97%, 100% and sensitivities of 100%, and 88%, 60%, 67%, respectively. The strength of agreement for the detection of resistance to INH was "substantial", compared between katG mutation and phenotypic INH only. Ion semiconductor NGS could make possible detection of several uncommon or novel amino acid changes in the full coding regions of these eight genes. However, molecular drug resistant profile should be complemented and validated by subsequent phenotypic DST studies at the same time.

Clinical and molecular characteristics of community-acquired Clostridium difficile infections in comparison with those of hospital-acquired C. difficile.

Community-acquired Clostridium difficile infection (CA-CDI) is a growing concern. CA-CDI differs from hospital-acquired C. difficile infection (HA-CDI) in its epidemiology, risk factors, severity, and outcomes. In this study, we investigated C. difficile infections in a tertiary care hospital in Seoul, Korea, and compared the CA-CDI and HA-CDI cases diagnosed in the same period. Total 593 cases were confirmed as CDI in 2014, of which CA-CDI accounted for 68 (11.5%) of the total CDI cases. Compared with HA-CDI, the mean age of CA-CDI cases was lower than that of HA-CDI (42.7 vs 60.4). In CA-CDI, antibiotic and proton pump inhibitor (PPI) use in the 12 preceding weeks and concurrent chemotherapy and tube feeding were less frequent compared with HA-CDI. In most cases (63/68, 92.6%), patients with CA-CDI recovered without any complications or recurrence. The most prevalent C. difficile type in CA-CDI cases was PCR-ribotype 012, accounting for 18.3% of the total, followed by PCR-ribotype 018 (16.7%).

Dynamics of bacterial communities in rice field soils as affected by different long-term fertilization practices.

Fertilization and the response of the soil microbial community to the process significantly affect crop yield and the environment. In this study, the seasonal variation in the bacterial communities in rice field soil subjected to different fertilization treatments for more than 50 years was investigated using 16S rRNA sequencing. The simultaneous application of inorganic fertilizers and rice straw compost (CAPK) maintained the species richness of the bacterial communities at levels higher than that in the case of non-fertilization (NF) and application of inorganic fertilizers only (APK) in the initial period of rice growth. The seasonal variation in the bacterial community structure in the NF and APK plots showed cyclic behavior, suggesting that the effect of season was important; however, no such trend was observed in the CAPK plot. In the CAPK plot, the relative abundances of putative copiotrophs such as Bacteroidetes, Firmicutes, and Proteobacteria were higher and those of putative oligotrophs such as Acidobacteria and Plactomycetes were lower than those in the other plots. The relative abundances of organotrophs with respiratory metabolism, such as Actinobacteria, were lower and those of chemoautotrophs that oxidize reduced iron and sulfur compounds were higher in the CAPK plot, suggesting greater carbon storage in this plot. Increased methane emission and nitrogen deficiency, which were inferred from the higher abundances of Methylocystis and Bradyrhizobium in the CAPK plot, may be a negative effect of rice straw application; thus, a solution for these should be considered to increase the use of renewable resources in agricultural lands.