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Land-use changes (LUC), primarily due to deforestation and soil disturbance, are one of the major causes of soil quality degradation and greenhouse gas emissions. Effects of LUC on soil physicochemical properties and changes in soil quality and land use management strategies that can effectively restore soil carbon and microbial biomass levels have been reported from all over the world, but the impact analysis of such practices in the Indian context is limited. In this study, over 1,786 paired datasets (for meta-analysis) on land uses (LUs) were collected from Indian literature (1990–2019) to determine the magnitude of the influence of LUC on soil carbon, microbial biomass, and other physical and chemical properties at three soil depths. Meta-analysis results showed that grasslands (36.1%) lost the most soil organic carbon (SOC) compared to native forest lands, followed by plantation lands (35.5%), cultivated lands (31.1%), barren lands (27.3%), and horticulture lands (11.5%). Our findings also revealed that, when compared to forest land, the microbial quotient was lower in other LUs. Due to the depletion of SOC stock, carbon dioxide equivalent (CO 2 eq) emissions were significantly higher in all LUs than in forest land. Results also showed that due to the conversion of forest land to cultivated land, total carbon, labile carbon, non-labile carbon, microbial biomass carbon, and SOC stocks were lost by 21%, 25%, 32%, 26%, and 41.2%, respectively. Changes in soil carbon pools and properties were more pronounced in surface (0–15 cm) soils than in subsurface soils (15–30 cm and 30–45 cm). Restoration of the SOC stocks from different LUs ranged from a minimum of 2% (grasslands) to a maximum of 48% (plantation lands). Overall, this study showed that soil carbon pools decreased as LUC transitioned from native forestland to other LUs, and it is suggested that adopting crop-production systems that can reduce CO 2 emissions from the intensive LUs such as the ones evaluated here could contribute to improvements in soil quality and mitigation of climate change impacts, particularly under Indian agro-climatic conditions.

Conversion of mangrove vegetation into rice cultivation is considerably enhanced nowadays which adversely affects ecological sustainability. Soil microbial community is one of the key indicators to monitor soil health in mangroves. Studies on the variations in the microbial community within mangroves are plenty, whereas reports in mangrove-converted paddy soils are scarce. Therefore, Biolog ® eco-plate-based technique was used in this study to assess soil microbial community in the Bhitarkanika (MB) and Sundarban (MS) sub-humid tropical mangroves-converted paddy soil. The results showed that significantly lower soil microbial biomass carbon and enzyme activities were recorded in MB and MS compared to the NRRI (National Rice Research Institute) paddy soil where continuous rice cultivation is being practiced conventionally since 1946 under the sub-humid tropical region. Biolog®-based average well color development (AWCD) was found significantly lower in MS and MB compared to NRRI. Shannon–Weaver and McIntosh indices followed the similar trends of AWCD. A biplot analysis indicated the positive correlation of pH, available phosphorus, actinomycetes population, and phenolic compound utilization under MS, whereas EC and phosphate-solubilizing bacteria were positively correlated under MB. Compared to MS and MB, NRRI paddy soil harbored more carbohydrate-utilizing microbes and showed a positive correlation with fluorescin-diacetate, dehydrogenase, and acid phosphatase. Overall, the present study suggested that the conversion of the Sundarban and Bhitarkanika mangroves into rice cultivation adversely affected the microbial diversity, thereby altering natural sustainability.

Cereal crop production gains under conventional agricultural systems in India have been declining in recent years because of inadequate management practices, creating a considerable concern. These activities were shown to deplete soil organic matter stocks, resulting in a decrease in microbial activity and soil organic carbon (SOC) content. Moreover, even with minimal use of organic sources in cultivated land, soil carbon status deteriorated, particularly in subtropical climates. Integrated nutrient management (INM), a modified farming method, has the potential to effectively utilize organic and inorganic resources, to improve the quality of soils and crops, and making farming more economically viable and sustainable. The aim of this study was to use meta-analysis to quantify the effects of INM on crop production, soil carbon, and microbial activity in Indian soils. During the years 1989–2018, data from various research studies in India, mainly on nutrient management in rice and wheat crops, were collected. Meta-Win 2.1 software was used to analyze the results, and significance was determined at p < 0.05. The results showed that the yield of rice and wheat was 1.4 and 4.9% more in INM than that in 100% NPK (N: nitrogen, P: phosphorous, and K: potassium), and that respective yields were comparatively higher in loamy soils (2.8%) and clayey soils (1.0%). The INM treatment increased SOC and microbial biomass carbon (MBC), resulting in improved overall soil quality. The SOC stock was increased by 23.8% in rice, 15.1% in wheat, 25.3% in loamy soils, and 14.4% in clayey soils in INM over 100% NPK. Microbial quotient (MQ) data showed significant trends between different management systems in both soil types, for example, INM > 100% NPK > No NPK. Due to more soil cracking and reduced aggregate stability in the rice field (greater short-term soil structural changes), the SOC stock loss in rice was higher than that in wheat. The CO 2 equivalent emissions were 7.9 Mg ha −1 higher in no NPK (control) than in 100% NPK, and 16.4 Mg ha −1 higher in control than in INM. In other words, INM increased soil carbon sequestration by 2.3 Mg ha −1 as compared to using 100% NPK. Overall, the findings of this study show that INM could be a viable farming system mode in India for improving crop production, increasing soil carbon sequestration, and improving microbial activity while remaining economically and environmentally sustainable.

Due to the introduction of zero-till wheat in the Indo-Gangetic plains (IGP) in India, irrigation and fertilizer nitrogen (N) management needs to be modified from that followed under conventionally tilled fields. A field experiment was conducted to study the effect of irrigation and N levels on yield and N uptake by zero-till wheat, fertilizer N-use efficiency, and distribution of nitrate-N (NO 3 -N) in a soil profile under zero-till conditions in an acidic alluvial soil of the eastern IGP. The experiment was laid out in a split-plot design with four levels of irrigation as main plots (I 0 -no irrigation, rain-fed, I 1 -122 mm in one irrigation at 21 days after sowing (DAS), I 2 -263 mm in two irrigations at 21 and 42 DAS, and I 3 -386 mm in three irrigations at 21, 42, and 84 DAS) and 4 N levels [0 (N 0 ), 60 (N 1 ), 120 (N 2 ), and 150 (N 3 ) kg N ha −1 ] as subplots. Grain and straw yields were significantly higher at the irrigation level-I 2 and 120 kg N ha −1 -N 2 over the control (I 0 and N 0 ) and were at par with the highest applied levels of irrigation and N (I 3 and N 3 ). The nitrogen uptake by wheat followed a trend similar to yield for irrigation levels; however, it increased significantly up to 150 kg N ha −1 . After the harvest of wheat crop, more NO 3 -N was observed in the 60–90 cm subsurface soil layer than in the surface 0–15 cm and/or 15–30 cm and 30–60 cm subsurface soil layers. The highest NO 3 -N concentration was recorded in the treatment I 2 N 2 . Accumulation of NO 3 -N in the soil increased up to irrigation levels I 2 and with increasing doses of fertilizer N application. Combined applications of irrigation and N had a positive and significant influence on agronomic efficiency (AE) and apparent N recovery (ANR) but had no significant effect on physiological efficiency (PE). This study suggests that an appropriate combination of irrigation and N levels in zero-till wheat can lead to not only high-yield levels and N-use efficiency but also adequately control NO 3 -N leaching under acidic alluvial soils in the eastern IGP.

Agroforestry systems (AFSs) have potential to combat climate change and to ensure food security. AFSs can sequester carbon and amend the organic matter, thereby enhancing the crop productivity. Carbon sequestration depends on the type of AFSs, climate, cropping pattern, and management practices. The aim of this study was to evaluate different AFSs for their potential to sequester carbon and impact on soil organic matter (SOM) in the eastern sub-Himalayas, India. Hedge-, alder-, and guava-based AFSs were established along with control (without any tree), and the maize–mustard–potato cropping pattern was followed in each AFS. Soil samples were collected after the fifth crop cycle and further analyzed. The results showed that crop productivity was significantly higher in all the AFSs than control. On average, soil organic carbon (SOC) was found to be significantly higher by 62 and 64% in hedge-based AFSs as compared to guava-based AFSs and control, respectively, and at par with alder-based AFSs. Particulate organic carbon (POC) was higher in all the three AFSs than in the control. For microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) contents, the trend of AFSs was expressed as alder-based AFS > hedge-based AFS > guava-based AFS > control. Hedge- and alder-based AFSs had higher SOC stocks than guava-based AFSs and control. Carbon dioxide equivalent (CO 2 eq.) emissions were greater in control than hedge-based AFSs (35.2 Mg ha −1 ), followed by alder-based AFSs (28.6 Mg ha −1 ), and the lowest was observed in guava-based AFSs. On an average, hedge species accumulated more nitrogen (N), phosphorus (P), and potassium (K), which were 60, 12, and 28 kg ha −1 yr −1 , respectively. This conclusively proved that AFSs were significantly affecting SOM pools and crop productivity and had a significant role in carbon retention in the soil. Overall, hedge- and alder-based AFSs retained higher soil carbon, and hence, hedge- and alder-based AFSs may be promoted to achieve climate-smart agriculture practices in the acid soils of the Indian sub-Himalayan region.

The microbe-mediated conversion of nitrate (NO3−) to ammonium (NH4+) in the nitrogen cycle has strong implications for soil health and crop productivity. The role of prokaryotes, eukaryotes and their phylogeny, physiology, and genetic regulations are essential for understanding the ecological significance of this empirical process. Several prokaryotes (bacteria and archaea), and a few eukaryotes (fungi and algae) are reported as NO3− reducers under certain conditions. This process involves enzymatic reactions which has been catalysed by nitrate reductases, nitrite reductases, and NH4+-assimilating enzymes. Earlier reports emphasised that single-cell prokaryotic or eukaryotic organisms are responsible for this process, which portrayed a prominent gap. Therefore, this study revisits the similarities and uniqueness of mechanism behind NO3− -reduction to NH4+ in both prokaryotes and eukaryotes. Moreover, phylogenetic, physiological, and genetic regulation also shed light on the evolutionary connections between two systems which could help us to better explain the NO3−-reduction mechanisms over time. Reports also revealed that certain transcription factors like NtrC/NtrB and Nit2 have shown a major role in coordinating the expression of NO3− assimilation genes in response to NO3− availability. Overall, this review provides a comprehensive information about the complex fermentative and respiratory dissimilatory nitrate reduction to ammonium (DNRA) processes. Uncovering the complexity of this process across various organisms may further give insight into sustainable nitrogen management practices and might contribute to addressing global environmental challenges.HighlightsDNRA is one of the potent beneficial pathways to maintain nitrogen pool in the system.Nitrate reduction is governed by both prokaryotes and eukaryotes.Evolutionary linkage between these organisms is also established for NO3- reduction to ammonium.F-DNRA needs energy through substrate-level phosphorylation, whereas R-DNRA through oxidative phosphorylation.Post-translational and epigenetic modifications are the major factors influencing NO3- reduction.

NrfA is the molecular marker for dissimilatory nitrate reduction to ammonium (DNRA) activity, catalysing cytochrome c nitrite reductase enzyme. However, the limited study has been made so far to understand the structural homology modeling of NrfA protein in DNRA bacteria. Therefore, three model DNRA bacteria (Escherechia coli, Wolinella succinogenes and Shewanella oneidensis) were chosen in this study for in-silico protein modeling of NrfA which roughly consists of similar length of amino acids and molecular weight and they belong to two contrasting taxonomic families (γ-proteobacteria with nrfABCDEFG and ε-proteobacteria with nrfHAIJ operon). Multiple bioinformatic tools were used to examine the primary, secondary, and tertiary structure of NrfA protein using three distinct homology modeling pipelines viz., Phyre2, Swiss model and Modeller. The results indicated that NrfA protein in E. coli, W. succinogenes and S. oneidensis was mostly periplasmic and hydrophilic. Four conserved Cys-X1-X2-Cys-His motifs, one Cys-X1-X2-Cys-Lys haem-binding motif and Ca ligand were also identified in NrfA protein irrespective of three model bacteria. Moreover, 11 identical conserved amino acids sequence was observed for the first time between serine and proline in NrfA protein. Secondary structure of NrfA revealed that α-helices were observed in 77.9%, 73.4%, and 77.4% in E. coli, W. succinogenes and S. oneidensis, respectively. Ramachandran plot showed that number of residue in favored region in E. coli, W. succinogenes and S. oneidensis was 97.03%, 97.01% and 97.25%, respectively. Our findings also revealed that among three pipelines, Modeller was considered the best in-silico tool for prediction of NrfA protein. Overall, significant findings of this study may aid in the identification of future unexplored DNRA bacteria containing cytochrome c nitrite reductase. The NrfA system, which is linked to respiratory nitrite ammonification, provides an analogous target for monitoring less studied N-retention processes, particularly in agricultural ecosystems. Furthermore, one of the challenging research tasks for the future is to determine how the NrfA protein responds to redox status in the microbial cells.

In the quest of achieving sustainable crop productivity, improved soil health, and increased carbon (C) sequestration in the soil, conservation agriculture (CA) is increasingly being promoted and adopted in the Indian subcontinent. However, because some researchers from different regions of the world have reported reduced crop yield under CA relative to agriculture based on conventional tillage (CT), a meta-analysis has been conducted based on published research from India to evaluate the effects of CA on the yield of crops, accumulation of soil organic C as an index of soil health, and C sequestration in the soil in different regions and soil textural groups in the country. The meta-analysis is based on 544 paired observations under CA and CT from 35 publications from India was carried out using Meta Win 2.1 software. The results showed an overall significant ( p  < 0.05) reduction of 1.15% crop yield under CA compared to CT. Yearwise data showed a reduction of yields under CA from 2009 to 2016, but an increase from 2017 to 2020. Yield reduction was observed in the eastern, north-eastern, and southern regions of India but in western, northern, and north-western regions of the country, an increase was observed under CA rather than CT. Sandy loam and clayey soils exhibited higher crop yield under CA than under CT. Compared to CT, soil organic C content and soil C sequestration under CA increased by 8.9% and 7.3%, respectively. Also, in all the regions and soil textural groups both soil organic C accumulation and soil C sequestration were higher under CA than under CT. Factors such as rainfall, soil depth, available nitrogen (N), and total N significantly influenced the extent of yield increase/decrease and soil organic C accumulation under CA. Overall, results of the meta-analysis suggest that the promotion of CA in India will have to be location-specific taking into consideration the crops, soil attributes, and climatic conditions. Graphical abstract

Rice-based integrated farming system improves the productivity and profitability by recycling resources efficiently. In the sub-humid tropics, rice production without sufficient nutrient replenishment often leads to soil health and fertility degradation. There has been very limited research on soil health and fertility after adopting a multi-enterprising rice-based integrated farming system (IFS), notably in the rice-fish-livestock and agroforestry system, when compared to a conventional farming system (CS). Therefore, the present study analyzed the dynamics of soil properties, soil bacterial community structure and their possible interaction mechanisms, as well as their effect on regulating soil quality and production in IFS, IFSw (water stagnant area of IFS) and CS. The results indicated that soil nutrient dynamics, bacterial diversity indices (Shannon index, Simpson index, Chao 1, ACE and Fisher index) and system productivity were higher in IFSw and IFS compared to CS. Moreover, relative operational taxonomic units of dominant bacterial genera ( Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, Cyanobacteria, Crenarchaeota and Gemmatimonadetes ) were also higher in IFSw and IFS compared to CS. Mean soil quality index (SQI) was highest in IFSw (0.780 ± 0.201) followed by IFS (0.770 ± 0.080) and CS (0.595 ± 0.244). Moreover, rice equivalent yields (REY) and rice yields were well correlated with the higher levels of soil biological indices (SQI Biol ) in IFS. Overall, our results revealed that rice-based IFS improved the soil health and fertility and ensuing crop productivity through positive interaction with soil bacterial communities and nutrient stoichiometry leading to agroecosystem sustainability.

The taxonomy of Azolla-cyanobiont is a long-term debate within the scientific community. Morphological and biochemicalbased reports indicated the presence of Anabaena, Nostoc and/or Trichormus azollae as abundant Azolla-cyanobionts, however, molecular data did not support the abundance of Anabaena and/or Nostoc. To understand furthermore, the cyanobiont diversity in six species of Azolla (A. microphylla, A. mexicana, A. filiculoides, A. caroliniana, A. pinnata and A. rubra) was analyzed based on 16S rRNA Illumina-MiSeq sequencing. Additionally, biomass and nutrient profiling of Azolla spp. were analyzed and correlated with cyanobiont diversity. Illumina-MiSeq data revealed that 99.6–99.9% of total operational taxonomic units (OTUs) belonged to Nostocophycideae (class), Nostocales (order) and Nostacaceae (family). At genus level, the unassigned affiliation (93.4–97.9%) under Nostacaceae family was abundant followed by Cylindrospermopsis OTUs (1.1–6.0%). Interestingly, A. pinnata harboured maximum Cylindrospermopsis OTUs and also recorded higher biomass (40.67 g m⁻² day⁻¹), whereas crude protein (25.9%) and antioxidants (76.9%) were recorded to be higher in A. microphylla. Biplot analysis revealed that A. pinnata and its cyanobiont abundance were positively correlated with neutral and acid detergent fibers. Overall, the present findings deepened the understanding about cyanobiont in Azolla and its relations with Azolla nutrient profiling.