Biology and Fertility of Soils最新文献

{"title":"Top-down gene upregulation and not microbial community diversity in explaining local-scale litter decomposition","authors":"Xingzhou Huang, Fangping Li, Fuzhong Wu, Xinying Zhang, Xiangyin Ni","doi":"10.1007/s00374-024-01857-2","DOIUrl":"https://doi.org/10.1007/s00374-024-01857-2","url":null,"abstract":"<p>Litter decomposition has historically been attributed to soil microbial community at local scale, but which fundamental process directly contributes to carbon release from decomposing litter remains not fully understood. Here we used in situ microcosms to assess the temporal changes in soil microbial biomass, taxonomic composition, alpha and beta diversity, network complexity and carbon-degrading functional genes during litter decomposition of a subtropical dominant species (<i>Castanopsis carlesii</i>) in an older (45-years) and a younger (9-years) evergreen broadleaved forests. The soil phospholipid fatty acids, bacterial and fungal community composition, α-diversity indexes and network topological properties were not changed significantly after short-term litter input when litter was decomposed by approximately 70%. However, the absolute abundance of functional genes involved in the decomposition of starch, pectin, hemicellulose, cellulose, chitin and lignin were up-regulated, and these variations were associated with soil α-1.4-glucosidase, β-glucosidase and cellobiohydrolase activities in contributing to litter carbon release during decomposition. These results suggest that the upregulation of functional genes rather than microbial community composition and diversity controls local-scale litter decomposition by encoding and secreting enzymes in these subtropical forests.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142013860","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Organic fertilization strengthens multiple internal pathways for soil mineral nitrogen production: evidence from the meta-analysis of long-term field trials","authors":"Ahmed S. Elrys, Shending Chen, Mengru Kong, Lijun Liu, Qilin Zhu, Xiaoqian Dan, Shuirong Tang, Yanzheng Wu, Lei Meng, Jinbo Zhang, Christoph Müller","doi":"10.1007/s00374-024-01856-3","DOIUrl":"https://doi.org/10.1007/s00374-024-01856-3","url":null,"abstract":"<p>Organic carbon based amendments can improve soil structure and fertility, as well as increase composition and diversity of soil microbial community. One of the major functions of improving soil fertility is to achieve effective nitrogen (N) management and mineralization. In this study, 746 paired observations were pooled from 20 long-term field experiments to verify the hypothesis that compared to synthetic only fertilization, long-term application of organic fertilization alone or in combination with synthetic fertilization could strengthen multiple internal pathways for soil N supply under various climatic conditions. We found that long-term application of synthetic N fertilizers alone or in combination with phosphorus (P) and potassium (K) led to an increase only in the recalcitrant organic N mineralization rate (<i>M</i>_Nrec) by 210% and 263%, respectively. However, long-term application of organic fertilizers alone or in combination with synthetic N fertilizers increased <i>M</i>_Nrec, labile organic N mineralization rate (<i>M</i>_Nlab) and release of adsorbed ammonium from cation exchange sites (<i>R</i>_NH4a) by 160% and 200%, 153% and 353%, and 1025% and 541%, respectively. This indicates that organic fertilization can strengthen multiple internal pathways for mineral N production. The long-term co-application of organic and synthetic fertilizers stimulated <i>M</i>_Nlab (197%), <i>M</i>_Nrec (151%) and <i>R</i>_NH4a (563%) in subtropical regions, but it had no effect on heterotrophic nitrification (<i>O</i>_Nrec). In contrast, it stimulated <i>M</i>_Nrec (505%), <i>R</i>_NH4a (633%) and <i>O</i>_Nrec (184%) in temperate regions, with no observed effect on <i>M</i>_Nlab. These data confirm that if one N supply source is shut-off under specific climatic conditions the other pathways continue to provide N. The meta-analysis advances our understanding of agroecosystems and as such help to improve frameworks for enhancing soil health.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-08-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141918835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"In situ soil imaging, a tool for monitoring the hourly to monthly temporal dynamics of soil biota","authors":"Emma Belaud, Christophe Jourdan, Dominique Barry-Etienne, Claire Marsden, Agnès Robin, Elisa Taschen, Mickael Hedde","doi":"10.1007/s00374-024-01851-8","DOIUrl":"https://doi.org/10.1007/s00374-024-01851-8","url":null,"abstract":"<p>The complexity of the opaque soil matrix is a major obstacle to studying the organisms that inhabit it. Fast technological progress now offers new possibilities for the monitoring of soil biodiversity and root growth, such as in situ soil imaging. This study presents the potential of soil imaging devices to investigate the temporal dynamics and spatial distribution of soil biological activity and their interactions. The soil imaging devices were buried in a truffle field located in the south of France and set up to capture images automatically every 6 h at 1200 dpi. For the first time, root growth, mycorrhizal colonization and invertebrate occurrences – for 16 taxa – were studied simultaneously on the images captured over 3 months (between May and July 2019). The peak in root growth occurred at the end of May and beginning of June, followed by a peak in ectomycorrhizal colonization in mid-June. For invertebrates, specific dynamics of activity were observed for each taxon, reflecting contrasting phenologies. The constructed network of co-occurrences between invertebrates shows a change in its structure over the period, with a reduction of connectance. At a fine scale, oak fine roots revealed temporally variable growth rates with higher values at night. This window on the opaque soil matrix addresses many methodological challenges by allowing the monitoring of soil biological activity in an integrative, dynamic and non-destructive way. This innovative in situ imaging tool opens new questions and new ways of answering long-standing questions in soil ecology.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141895458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Activity of anaerobic methane oxidation driven by different electron acceptors and the relative microbiome in paddy fields across various rice growth periods and soil layers","authors":"Yuling Yang, Lidong Shen, Caiyu Geng, Bingjie Ren, Yanan Bai, Jinghao Jin, Wangting Yang","doi":"10.1007/s00374-024-01855-4","DOIUrl":"https://doi.org/10.1007/s00374-024-01855-4","url":null,"abstract":"<p>Currently, little is understood about the role of different anaerobic oxidation of methane (AOM) pathways and their relative contributions in reducing CH₄ emissions from rice fields. The potential rates of AOM caused by nitrate-, iron-, and sulfate-reduction, as well as the anaerobic methanotrophic (ANME-2d) archaeal absolute abundance and community composition were investigated across varying rice growth periods (tillering, jointing, flowering, and maturing) and soil layers (0–10, 10–20, 20–30, and 30–40 cm). The average potential rate of nitrate-AOM (2.73 nmol ¹³CO₂ g^-1 d^-1) was significantly higher than those of iron- (1.15 nmol ¹³CO₂ g^-1 d^-1) and sulfate-AOM (0.42 nmol ¹³CO₂ g^-1 d^-1) across growth periods and soil layers. The AOM rates in surface soils (0–20 cm) and earlier periods (tillering and jointing) were significantly higher than those in deep soils (20–40 cm) and later periods (flowering and maturing), respectively. Differently, ANME-2d archaeal absolute abundance and community compositions were only significantly affected by soil layers, with the highest absolute abundance in the 10–20 cm layer. The organic carbon content and availability of electron acceptor were the primary factors governing the rates of different AOM pathways and community of ANME-2d archaea. Overall, this study provided the variation in AOM rates driven via multiple electron acceptors and ANME-2d archaeal community across rice growth periods and soil layers, and provided an important scientific basis for precise quantification of AOM as a potential CH₄ sink in rice fields.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-08-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141895459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Varying soil moisture and pH with alpine meadow degradation affect nitrogen preference of dominant species","authors":"Chimin Lai, Qiwu Hu, Jianbo Sun, Chengyang Li, Xiaojie Chen, Ben Chen, Xian Xue, Ji Chen, Fujiang Hou, Gang Xu, Wuchen Du, Carly Stevens, Fei Peng, Jun Zhou","doi":"10.1007/s00374-024-01853-6","DOIUrl":"https://doi.org/10.1007/s00374-024-01853-6","url":null,"abstract":"<p>While it is established that dominant plant species of alpine meadows showed differential preference for N forms (ammonia, nitrate, and amino acids) under various degradation stages, the perseverance of the N-uptake preference and its affecting factors remains unknown. This is an important consideration because it determines efficacy of nutrient additions for restoration of degraded alpine meadows. An indoor pot experiment was conducted to investigate the plasticity and determinants of different plant species’ N-uptake preference using ¹⁵N-labeled inorganic N (¹⁵NH₄⁺ and ¹⁵NO₃⁻) and one of dual-labeled (¹³C-¹⁵N) amino acid (glycine). In the experiment, dominant species of alpine meadow from specific degradation status were planted in soils of alpine meadows with three different degradation status. Most species preferred to uptake nitrate in all soils, except the <i>Kobresia humilis</i>, <i>Carex moorcroftii</i>, and <i>Aster flaccidus</i> planted in the soil of severely degraded alpine meadow (SD-soil) that take up more ammonia. The relative abundance of different available N forms directly affects the N-uptake preferences of all species. The partial correlations between percentage uptake and availability of various N forms were different with the zero-order correlations when either soil moisture or pH was controlled. Differences in soil moisture and pH among the three alpine meadows affects the N uptake preference of the nine species through their impacts on the relative abundance of different available N forms. In conclusion, the differences in soil moisture and pH among soils of alpine meadows under different degradation statuses influence the relative abundance of various available N forms, thereby affecting the plant N uptake.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141880295","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of several long-term soil health treatments on populations of Pratylenchus penetrans and the soil microbial community","authors":"Els Nijhuis, Viola Kurm, Johnny Visser, Gerard Korthals, Leo van Overbeek","doi":"10.1007/s00374-024-01854-5","DOIUrl":"https://doi.org/10.1007/s00374-024-01854-5","url":null,"abstract":"<p>Soil suppressiveness can reduce the damage by plant parasitic nematodes (PPN) in agricultural soils and is conveyed by the activity of soil microorganisms. While natural suppressiveness has been reported, it is still poorly understood if soil suppressiveness can be elicited by manipulating the soil microbial community. In the present study we assessed the number of the <i>Pratylenchus penetrans</i> (Pp) and the bacterial and fungal community composition over 7 years in a long-term soil health experiment. The field experiment consisted of an organic and conventional agricultural land management system and three soil health treatments (SHT): an untreated control (CT), anaerobic disinfestation (AD) and a combination of marigold cover cropping, compost and chitin amendment (CB). The land management systems were kept continuously, while the soil health treatments were applied only twice in seven years. The microbial community significantly differed between the organic and conventional system, but there was no significant difference in Pp numbers between the two systems. However, both the CB treatment and to a lesser extent the AD treatment reduced Pp numbers and increased yield with the effect being the strongest in the years immediately after the treatment. Accordingly, both the bacterial and fungal community differed significantly between the treatments, the differences being largest in the years after the treatments. Notably, the CB treatment elicited both long-term changes in the microbial community and a reduction of Pp numbers lasting for at least three years. These results indicated that a combination of treatments can lead to an altered soil microbial community in combination with persisting suppressiveness of Pp.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141857630","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Investigating protistan predators and bacteria within soil microbiomes in agricultural ecosystems under organic and chemical fertilizer applications","authors":"Chen Liu, Zeyuan Zhou, Shuo Sun, Qi Zhang, Shiqi Sun, Xinnan Hang, Mohammadhossein Ravanbakhsh, Zhong Wei, Rong Li, Shimei Wang, Wu Xiong, George A. Kowalchuk, Qirong Shen","doi":"10.1007/s00374-024-01845-6","DOIUrl":"https://doi.org/10.1007/s00374-024-01845-6","url":null,"abstract":"<p>Organic farming can enhance biodiversity and soil health and is a sustainable alternative to conventional farming. Yet, soil protists especially protistan predators, have received inadequate attention, and their contributions to the sustainability of organic farming remained underexplored. In this study, we examined soil microbial communities from 379 samples, including both organic and chemically fertilized soils from China. Our findings revealed higher bacterial diversity and increases in plant-beneficial bacteria in organically farmed soils. Notably, organic farming systems facilitated dynamic predator-prey interactions, which may be disrupted by the application of chemical fertilizers. Additionally, organic farming enriched protistan predators, enhancing the relative abundance of functional PGPR, thus improving soil health. We further conducted a case study highlighting the critical role of organic matter in sustaining protistan predator populations and their interactions with bacteria. We propose the crucial contributions of organic inputs for supporting protistan predators and the interplay of predator-prey, ultimately enhancing soil functions and promoting agricultural sustainability.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-07-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141730640","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Characterization of microbial communities assimilating rhizosphere-deposited carbon in a soybean/maize intercropping system using the DNA-SIP technique","authors":"Fuyun Gao, Huiling Lai, Hao Su, Stephen J. Chapman, Yaying Li, Huaiying Yao","doi":"10.1007/s00374-024-01852-7","DOIUrl":"https://doi.org/10.1007/s00374-024-01852-7","url":null,"abstract":"<p>Legume/cereal intercropping is an example of classic nitrogen-efficient planting that can effectively improve crop yield and nutrient-utilization efficiency. However, the interaction between rhizosphere microorganisms and rhizodeposition and the related ecological mechanisms remain unclear. We conducted a pot experiment using ¹³CO₂ continuous labeling, DNA stable isotope probe technology, high-throughput sequencing, and the carbon-nitrogen-phosphorus functional gene chip to effectively track rhizosphere-deposited C and compare the microorganisms that utilize this C pool in the rhizosphere of a soybean/maize intercropping system at 21 days after labeling. The relative abundance of <i>Caldalkalibacillus</i> and <i>Nesterenkonia</i> that use rhizosphere-deposited C was significantly higher in the soybean/maize intercropping system than in monocropped soybean, but there were no significant differences between intercropped and monocropped maize. The soybean/maize intercropping system altered the composition of the microbial community that utilizes rhizosphere-deposited C and reduced the community richness. Moreover, intercropping improved the expression of functional genes associated with carbon fixation (<i>acsH</i> and <i>exg</i>) and nitrous oxide reduction (<i>nosZ1</i>). Overall, by tracking the flow of C from plant photosynthetic products to root exudates, our research provides new insights into identifying the microbial communities that assimilate and deposit carbon in soil.</p>","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141725761","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteria from the rhizosphere of a selenium hyperaccumulator plant can improve the selenium uptake of a non-hyperaccumulator plant","authors":"Huan Zhang, Dandan Yang, Chengxiao Hu, Xiaoping Du, Lianming Liang, Xu Wang, Guangyu Shi, Chuang Han, Yanni Tang, Zheng Lei, Ceng Yi, Xiaohu Zhao","doi":"10.1007/s00374-024-01846-5","DOIUrl":"https://doi.org/10.1007/s00374-024-01846-5","url":null,"abstract":"<p>It is unknown whether soil microbiota and soil bacteria isolated from the rhizosphere of selenium hyperaccumulator plants can affect selenium absorption by selenium non-hyperaccumulator plants. Here, we used pot experiments and split root experiments to investigate the role of soil microbiota and isolated rhizosphere bacteria from a selenium hyperaccumulator plant (<i>Cardamine violifolia</i>) in affecting selenium absorption by a selenium non-hyperaccumulator plant (<i>Brassica napus</i>), combining root metabolism analysis, microbiome profiling, strain isolation and its selenium absorption functional validation. We found that soil microbiota of <i>Cardamine violifolia</i> significantly increased the root selenium content by 31.8% and regulated root exudation by <i>Brassica napus.</i> Additionally, the application of upregulated long-chain organic acids + amino acids, long-chain organic acids + short-chain organic acids, ethanolamine, and 2-ketobutyric acid increased the selenium contents in the roots of <i>Brassica napus</i> by 69.6%, 38.4%, 81.2%, and 48.8%, respectively<i>.</i> Further investigation revealed that dominant bacteria were significantly enriched in the rhizosphere of <i>C. violifolia</i> compared to <i>B. napus.</i> After that, we isolated the rhizosphere bacteria of <i>Cardamine violifolia</i> and observed that <i>Bacillus</i> sp.-2, <i>Chryseobacterium</i> sp., and <i>Pseudomonas</i> sp., as well as their combined communities, significantly improved selenium absorption in <i>Brassica napus.</i> Moreover, the combined bacterial communities significantly regulated specific-root metabolism, enhanced rhizosphere soil available selenium content, promoted root development, increased expression levels of genes encoding selenium transporter in root. These findings provide insights into utilizing rhizosphere bacteria of selenium hyperaccumulator plants to increase selenium absorption by non-hyperaccumulator plants. </p><h3 data-test=\"abstract-sub-heading\">Graphical Abstract</h3>\u0000","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":6.5,"publicationDate":"2024-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141631313","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial: Recent advances in biology and fertility studies of paddy field soil","authors":"Susumu Asakawa, M. Nishida, T. Adhya, Kazuyuki Inubushi","doi":"10.1007/s00374-024-01850-9","DOIUrl":"https://doi.org/10.1007/s00374-024-01850-9","url":null,"abstract":"","PeriodicalId":9210,"journal":{"name":"Biology and Fertility of Soils","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-07-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141645772","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}