Bacterial and fungal contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

Wilhelm, Roland C.; Singh, Rahul; Eltis, Lindsay D.; Mohn, William W.

doi:10.1101/387308

Cited by 6 publications

(3 citation statements)

References 76 publications

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“…The microbial community changes produced during bioremediation (BS microcosms) reflected substrate consumption, where members of Actinomycetales and Sphingomonadales were gradually replaced by Caulobacterales, Xanthomonadales, Verrucomicrobiales, and Opitutales. Caulobacterales members were reported as lignocellulosic polymers degraders (Wilhelm et al 2018), Xanthomonadales included hydrocarbon degraders as well as generalist microorganisms (Gutierrez 2019), Verrucomicrobiales was suggested as aerobic organotrophic specialist (Chen et al 2020), while Opitutales members were described as harboured of genes related to C-source utilization and N cycling (Hester et al 2018).…”

Section: Discussionmentioning

confidence: 99%

Effects of organic matter addition on chronically hydrocarbon‐contaminated soil

et al. 2021

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Soil is the recipient of organic pollutants as a consequence of anthropogenic activities. Hydrocarbons are contaminants that pose a risk to human and environmental health. Bioremediation of aging contaminated soils is a challenge due to the low biodegradability of contaminants as a result of their interaction with the soil matrix. The aim of this work was to evaluate the effect of both composting and the addition of mature compost on a soil chronically contaminated with hydrocarbons, focusing mainly on the recovery of soil functions and transformations of the soil matrix as well as microbial community shifts. The initial pollution level was 214 ppm of polycyclic aromatic hydrocarbons (PAHs) and 2500 ppm of aliphatic hydrocarbons (AHs). Composting and compost addition produced changes on soil matrix that promoted the release of PAHs (5.7 and 15 % respectively) but not the net PAH elimination. Interestingly, composting stimulated AHs elimination (about 24 %). The lack of PAHs elimination could be attributed to the insufficient PAHs content to stimulate the microbial degrading capacity, and the preferential consumption of easily absorbed C sources by the bacterial community. Despite the low PAH catabolic potential of the aging soil, metabolic shift was driven by the addition of organic matter, which could be monitored by the ratio of Proteobacteria to Actinobacteria combined with E 4 /E 6 ratio. Regarding the quality of the soil, the nutrients provided by the exogenous organic matter contributed to the recovery of the

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Section: Discussionmentioning

confidence: 99%

Effects of organic matter addition on chronically hydrocarbon‐contaminated soil

et al. 2021

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“…In this regard, the increases recorded for ARC application were higher than the corresponding ones attained for PRC addition. Probably, the rice straw which is mainly used for PRC is of relatively low degradation (Wu et al, 2019) because it is rich in lignocellulose (El-Akhdar et al, 2018) which is a complicated substrate for enzymes (Andlar et al, 2018;Wilhelm et al, 2019). __________________________________________________________________________________________________________________ ________________________________________________ Egypt.…”

Section: Effect Of Animal and Plant Residue Composts On Plant Growth ...mentioning

confidence: 99%

Composting Animal and Plant Residues for Improving the Characteristics of a Clayey Soil and Enhancing the Productivity of Wheat Plant Grown Thereon

S.Hussein

Ali²,

Abbas³

et al. 2022

Egypt.J. Soil Sci.

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Wheat is a strategic crop in Egypt. Its local consumption is increasing continuously accordingly; Egypt has become the largest wheat importer worldwide. The sustainable approach for increasing wheat productivity is probably through organic additives. For this reason, animal, chicken and plant residues were collected from an experimental farm for preparation of (1) plant residue compost (PRC) via composting a mixture of air-dried and chopped rice and soybean straw at a rate of 1:1 and (2) animal residue compost (ARC) via composting a mixture of chicken and cattle manure at a rate of 1:1. The main aim of this study is to compare between the implications of amending a clayey soil with animal versus plant residues for improving soil physical and chemical characteristics. Also, this study considers the changes in soil fertility owing to these additives, hence their outcomes on wheat growth and productivity. To achieve this goal, a field investigation was conducted following a split-split design in which the two types of composts were plotted in main plots while the rates of compost application (15 and 25 Mg per hectare) were plotted in subplots. Non-amended control plots were also included for data comparison. All plots were cultivated with wheat seeds in winter 2018 and received the recommended doses of NPK fertilizers to compare between the two types of composts as conditioners not as fertilizers. The experiment lasted for 160 days until maturity. All composts improved considerably soil physical (soil bulk density, total porosity, saturated hydraulic conductivity and penetration resistance) and chemical (soil organic matter and CEC) characterises, especially with increasing their rate of application. In this concern, the results of the two types of composts were comparable. Also, these additives boosted grain and straw yields, yield components (spike length, spike weight, number of spikelets/ spike, 100-grain weight). Moreover, theyenriched soils with N, P, K, Fe, Mn, Zn and Cu in available forms; hence raised their contents within wheat shoots and grains, with superiority for ARC versus PRC. There were significant positive correlations between shoot and grain yields in relation to the nutritional status of these plant parts. Accordingly, organic additives, especially animal residues, should be included in the coming sustainable approaches for increasing wheat production.

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“…In contrast, only a few types of bacteria degrade all lignocellulosic polymers, while most typically target simple soluble compounds (de Boer and van der Wal, 2008). Therefore, the role of bacteria in the decomposition of more recalcitrant 65 material is still debated (Wilhelm et al, 2018). However, still little is known on how microbial communities specialise in litter types with different physical and chemical traits (Freschet et al, 2011;Pioli et al, 2020).…”

Section: Introduction 45mentioning

confidence: 99%

Pairing litter decomposition with microbial community structures using the Tea Bag Index (TBI)

Daebeler

Petrová

Kinz³

et al. 2021

Preprint

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Abstract. Including information about soil microbial communities into global decomposition models is critical for predicting and understanding how ecosystem functions may shift in response to global change. Here we combined a standardised litter bag method for estimating decomposition rates, Tea Bag Index (TBI), with high-throughput sequencing of the microbial communities colonising the plant litter in the bags. Together with students of the Federal College for Viticulture and Fruit Growing, Klosterneuburg, Austria, acting as citizen scientists, we used this approach to investigate the diversity of prokaryotes and fungi colonising recalcitrant (rooibos) and labile (green tea) plant litter buried in three different soil types and during four seasons with the aim of (i) comparing litter decomposition [decomposition rates (k) and stabilisation factors (S)] between soil types and seasons, (ii) comparing the microbial communities colonising labile and recalcitrant plant litter between soil types and seasons (iii) correlating microbial diversity and taxa relative abundance patterns of colonisers with litter decomposition rates (k)and stabilisation factors (S). Stabilisation factor (S), but not decomposition rate (k), correlated with the season and was significantly lower in the summer. This finding highlights the necessity to include colder seasons in the efforts of determining decomposition dynamics in order to quantify nutrient cycling in soils accurately. With our approach, we further showed selective colonisation of plant litter by fungal and prokaryotic taxa sourced from the soil. The community structures of these microbial colonisers differed most profoundly between summer and winter, and rooibos litter was generally a stronger selector than green tea litter. Moreover, this study indicates an equal, if not higher, importance of fungal versus prokaryotic degraders for recalcitrant and labile plant litter decomposition. Our results collectively demonstrate the importance of analysing decomposition dynamics over multiple seasons and isolating the effect of the active component of the microbial community.

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Bacterial and fungal contributions to delignification and lignocellulose degradation in forest soils with metagenomic and quantitative stable isotope probing

Cited by 6 publications

References 76 publications

Effects of organic matter addition on chronically hydrocarbon‐contaminated soil

Effects of organic matter addition on chronically hydrocarbon‐contaminated soil

Composting Animal and Plant Residues for Improving the Characteristics of a Clayey Soil and Enhancing the Productivity of Wheat Plant Grown Thereon

Pairing litter decomposition with microbial community structures using the Tea Bag Index (TBI)

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