Biodiversity and biological degradation of soil

Scientific Reports, 2017

Maize inoculation by Azospirillum stimulates root growth, along with soil nitrogen (N) uptake and root carbon (C) exudation, thus increasing N use efficiency. However, inoculation effects on soil N-cycling microbial communities have been overlooked. We hypothesized that inoculation would (i) increase roots-nitrifiers competition for ammonium, and thus decrease nitrifier abundance; and (ii) increase roots-denitrifiers competition for nitrate and C supply to denitrifiers by root exudation, and thus limit or benefit denitrifiers depending on the resource (N or C) mostly limiting these microorganisms. We quantified (de)nitrifiers abundance and activity in the rhizosphere of inoculated and non-inoculated maize on 4 sites over 2 years, and ancillary soil variables. Inoculation effects on nitrification and nitrifiers (AOA, AOB) were not consistent between the three sampling dates. Inoculation influenced denitrifiers abundance (nirK, nirS) differently among sites. In sites with high C limitation for denitrifiers (i.e. limitation of denitrification by C > 66%), inoculation increased nirS-denitrifier abundance (up to 56%) and gross N 2 O production (up to 84%), likely due to increased root C exudation. Conversely, in sites with low C limitation (<47%), inoculation decreased nirS-denitrifier abundance (down to −23%) and gross N 2 O production (down to −18%) likely due to an increased roots-denitrifiers competition for nitrate. The rhizosphere provides a peculiar environment where a huge variety of positive, negative and neutral interactions between roots and microorganisms occur 1. Such interactions can significantly influence plant growth as well as the functioning, the abundance and the diversity of rhizospheric microbial communities 2. Beneficial interactions are known to be established by plant growth-promoting rhizobacteria, PGPRs, with host plants through several mechanisms, including associative N 2 fixation, phosphate solubilization or phytosiderophore production 3, 4. This can result in improved root growth 5, 6 , increased number and length of lateral roots 7 , as well as an increased root and shoot biomass 8, 9 and physiology 10. The better root development induced by inoculation can consequently enhance nutrient 11 and water 12 uptake by plant, stimulate ion transport systems in root 13 and increase the amount of root carbon, C, exudation 14, 15. Azospirillum spp. are well-known PGPRs that are able to colonize the roots of many crop plant species including maize 16, 17. These PGPRs produce phytohormones that can promote root growth and improve nutrient and water absorption by plants 18-21. In particular, inoculation of cereal crops by PGPRs like the well-studied Azospirillum lipoferum CRT1 is often expected to improve crop capacity to retrieve mineral nitrogen, N, from soil. This could pave the way for improving the sustainability of these cropping systems under low N inputs conditions 8. However, inoculated plants could differently affect N dynamics in their rhizosphere, thus influencing the levels and types of mineral N forms available and possibly N losses from soil through leaching of nitrate, NO 3 − , or emission of nitrous oxide, N 2 O, a potent greenhouse gas 22 .

1986

1976

The major portion of the global nitrogen cycle occurs between vegetation and soil, only minor ex- changes generally taking place with the atmosphere and the hydrosphere. Nitrogen conversions in soil are briefly reviewed and a global flow chart for soil nitrogen is presented. The turnover times of nitro- gen in various components of this global system are compared with its

Management of Nitrogen and Phosphorus Fertilizers in Sub-Saharan Africa, 1986

The ISME Journal, 2011

The two-step nitrification process is an integral part of the global nitrogen cycle, and it is accomplished by distinctly different nitrifiers. By combining DNA-based stable isotope probing (SIP) and high-throughput pyrosequencing, we present the molecular evidence for autotrophic growth of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB) in agricultural soil upon ammonium fertilization. Time-course incubation of SIP microcosms indicated that the amoA genes of AOB was increasingly labeled by 13 CO 2 after incubation for 3, 7 and 28 days during active nitrification, whereas labeling of the AOA amoA gene was detected to a much lesser extent only after a 28-day incubation. Phylogenetic analysis of the 13 C-labeled amoA and 16S rRNA genes revealed that the Nitrosospira cluster 3-like sequences dominate the active AOB community and that active AOA is affiliated with the moderately thermophilic Nitrososphaera gargensis from a hot spring. The higher relative frequency of Nitrospira-like NOB in the 13 C-labeled DNA suggests that it may be more actively involved in nitrite oxidation than Nitrobacter-like NOB. Furthermore, the acetylene inhibition technique showed that 13 CO 2 assimilation by AOB, AOA and NOB occurs only when ammonia oxidation is not blocked, which provides strong hints for the chemolithoautotrophy of nitrifying community in complex soil environments. These results show that the microbial community of AOB and NOB dominates the nitrification process in the agricultural soil tested.

Biology and Fertility of Soils, 1991

Soil Science Society of America Journal, 2010

All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. Nitrogen Transformations and Microbial Communities in Soil Aggregates from Three Tillage Systems Soil Biology & Biochemistry N o-till has several advantages over tilled systems, including increased water infi ltration, greater sequestration of soil organic matter, and reduction of soil erosion. Additionally, a body of literature has also demonstrated that soil N retention is greater in no-till than tilled systems (Alvarez et al., 1998; Beare et al., 1997). Plant-available N is not well defi ned for no-till systems, however, because during the transition from conventional tillage to no-till, particularly when C is accruing, increased microbial immobilization of inorganic N (Kitur et al., 1984; Rice and Smith, 1984) may temporarily reduce the plant-available N. As N immobilization and mineralization processes become more balanced, N availability to plants may become greater in no-till than in tilled soils (Rice et al., 1986). Information about the internal N cycle of no-till soils is limited. Th erefore, a thorough understanding of N cycling processes is required for formulation of the best N management practices in long-term no-till systems. Microbially mineralized NH 4 or NO 3 is also concurrently immobilized by soil microorganisms and recycled into the inorganic N pool due to the rapid turnover rate of the soil microbial biomass. Th us, the N dynamics resulting from the balance between mineralization and immobilization of inorganic N (both

European Journal of Soil Biology, 2016

Organic fertilizers are of high interest in agriculture as they promise a retarded release of the nitrogen to soil, which improves uptake efficiency by plants and reduces negative impacts like the formation of nitrate by nitrifiers or N 2 O by denitrifying microorganisms. In this study we tested the effects of seven different commercially available organic fertilizers of plant-, animal-, or microbial origin in a two-month greenhouse trial, using the perennial grass Cynodon dactylon in pots and monitoring effects on plant growth as well as on the abundance of prokaryotic nitrifiers and denitrifiers by realtime PCR. In most cases a single application of the fertilizers induced plant growth but did not increase the abundance of nitrifiers and denitrifiers. In contrast a repeated application stimulated, in addition to plant growth, also the increase of the two functional groups studied and a faster mobilization of nitrogen from the different fertilizers. Upon analyzing total bacterial DNA extracted from soil nirK abundance was found responsive to plant presence. Bacterial amoA and nosZ gene copies were significantly positively correlated with plant growth and cumulative dry weight at harvest. The latter was responsive as early as 9 days after fertilizer supplementation.

Plant and Soil, 1989

The possibility is examined that carbon (C) released into the soil from a root could enhance the availability of inorganic nitrogen (N) to plants by stimulating microbial activity. The release of soluble C compounds from roots is assumed to occur by one of two general processes: cortical cell death or exudation from intact cells. On the basis of several assumptions chosen to allow maximal amounts of N mineralisation to be calculated, greater amounts of net N mineralisation are theoretically possible at realistic soil C:N ratios if bacteria are grazed by predators such as protozoa, than if bacteria alone are active. More N is mineralised when the substrate released from the root has a high C:N ratio (as in cell death) than when it is relatively N-rich. The amounts of N that a root might realistically cause to be mineralised are unlikely to account entirely for high nitrate inflow rates that have been measured experimentally. However there are circumstances in which the loss of C from roots is essential if any N is to be mineralised and obtained by plants.

Agronomy, 2015

Agriculture is responsible for over half of the input of reactive nitrogen (N) to terrestrial systems; however improving N availability remains the primary management technique to increase crop yields in most regions. In the majority of agricultural soils, ammonium is rapidly converted to nitrate by nitrification, which increases the mobility of N through the soil matrix, strongly influencing N retention in the system. Decreasing nitrification through management is desirable to decrease N losses and increase N fertilizer use efficiency. We review the controlling factors on the rate and extent of nitrification in agricultural soils from temperate regions including substrate supply, environmental conditions, abundance and diversity of nitrifiers and plant and microbial interactions with nitrifiers. Approaches to the management of nitrification include those that control ammonium substrate availability and those that inhibit nitrifiers directly. Strategies for controlling ammonium substrate availability include timing of fertilization to coincide with rapid plant update, formulation of fertilizers for slow release or with inhibitors, keeping plant growing continuously to assimilate N, and intensify internal N cycling (immobilization). Another effective strategy is to inhibit nitrifiers directly with either synthetic or biological nitrification inhibitors. Commercial nitrification inhibitors are effective but their use is complicated by a changing climate and by organic management requirements. The interactions of the nitrifying organisms with plants or microbes producing biological nitrification inhibitors is a promising approach but just beginning to be critically examined. Climate smart agriculture will need to carefully consider optimized seasonal timing for these strategies to remain effective management tools.