Sep 2022, Volume 4 Issue 3

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    Rishikesh Singh, Tanu Kumari, Pramit Verma, Bhupinder Pal Singh, Akhilesh Singh Raghubanshi

    • Resource-conservation practices are emerging for attaining sustainability in agriculture.

    • The research is now progressing towards combined application of emergent agronomic practices.

    • Role of agro-climatic zones is imperative in developing compatible agronomic packages.

    • Compatible agriculture packages may help in buffering the yield penalty occurred one system.

    • Compatible agriculture packages would be the need for attaining true sustainability in agriculture.

    Besides contributing majorly in the growth of a country, agriculture is one of the severely affected sectors at present. Several modifications and adaptations are being made in agricultural practices to cope-up with the declining soil fertility and changing climate scenarios across the world. However, the development and adoption of a single agricultural practice may not help in the holistic mitigation of the impacts of climate change and may result in economic vulnerability to farmers. Therefore, it is high time to develop and recommend a group of agricultural practices i.e. package-based agriculture system having some compatibility for one another in the long term. In this article, a viewpoint has been given on some emergent agronomic practices adopted in the tropical agro-ecosystems which have potential to be developed as compatible agricultural package in combination. Moreover, we also emphasized on exploring some key indicators/environmental factors to assess the compatibility of different agronomic practices. For identifying the research transition from single to combined agricultural practices, a bibliometric analysis was performed by using conservation agriculture (CA), the system of rice intensification (SRI), organic agriculture and soil (biochar) amendment as the major agronomic practices being used for improving agro-ecological services such as improving nutrient cycling, soil fertility and crop productivity as well as climate change mitigation. The results revealed that scientific communities are now paying attention to exploring the role of combined agricultural practices for agro-ecological balance and climate change adaptation. Moreover, the limitations of the adoption of agronomic packages under different agro-climatic zones have also been highlighted. The recommendations of the study would further help the environmental decision-makers to develop potential measures for climate change mitigation without compromising the agro-ecological balance.

    Xiongkun Zhang, Shan Wu, Xiaojie Sun, Monika Mortimer, Yichao Wu, Ming Zhang, Qiaoyun Huang, Peng Cai

    1. Basic principles of microfluidics are introduced

    2. Microfluidics to study bacterial spatial distribution and functions

    3. Challenges of microfluidics for soil microbiome in future

    Microfluidics confers unique advantages in microbiological studies as these devices can accurately replicate the micro- and even nano-scale structures of soil to simulate the habitats of bacteria. It not only helps us understand the spatial distribution of bacterial communities (such as biofilms), but also provides mechanistic insights into microbial behaviors including chemotaxis and horizontal gene transfer (HGT). Microfluidics provides a feasible means for real-time, in situ studies and enables in-depth exploration of the mechanisms of interactions in the soil microbiome. This review aims to introduce the basic principles of microfluidic technology and summarize the recent progress in microfluidic devices to study bacterial spatial distribution and functions, as well as biological processes, such bacterial chemotaxis, biofilm streamers (BS), quorum sensing (QS), and HGT. The challenges in and future development of microfluidics for soil microbiological studies are also discussed.

    Shuzhen Li, Xiongfeng Du, Kai Feng, Yueni Wu, Qing He, Zhujun Wang, Yangying Liu, Danrui Wang, Xi Peng, Zhaojing Zhang, Arthur Escalas, Yuanyuan Qu, Ye Deng

    • Roughly 15 919 to 56 985 prokaryotic species inhabited in 1 m2 grassland topsoil.

    • Three clustering tools, including DADA2, UPARSE and Deblur showed huge differences.

    • Nearly 500 000 sequences were required to catch 50% species.

    • Insufficient sequencing depth greatly affected observed and estimated richness.

    • Higher order of Hill numbers reached saturation with fewer than 100 000 sequences.

    Due to the tremendous diversity of microbial organisms in topsoil, the estimation of saturated richness in a belowground ecosystem is still challenging. Here, we intensively surveyed the 16S rRNA gene in four 1 m2 sampling quadrats in a typical grassland, with 141 biological or technical replicates generating over 11 million sequences per quadrat. Through these massive data sets and using both non-asymptotic extrapolation and non-parametric asymptotic approaches, results revealed that roughly 15 919±193 27 193±1076 and 56 985±2347 prokaryotic species inhabited in 1 m2 topsoil, classifying by DADA2, UPARSE (97% cutoff) and Deblur, respectively, and suggested a huge difference among these clustering tools. Nearly 500 000 sequences were required to catch 50% species in 1 m2, while any estimator based on 500 000 sequences would still lose about a third of total richness. Insufficient sequencing depth will greatly underestimate both observed and estimated richness. At least ~911 000, ~3 461 000, and ~1 878 000 sequences were needed for DADA2, UPARSE, and Deblur, respectively, to catch 80% species in 1 m2 topsoil, and the numbers of sequences would be nearly twice to three times on this basis to cover 90% richness. In contrast, α-diversity indexes characterized by higher order of Hill numbers, including Shannon entropy and inverse Simpson index, reached saturation with fewer than 100 000 sequences, suggesting sequencing depth could be varied greatly when focusing on exploring different α-diversity characteristics of a microbial community. Our findings were fundamental for microbial studies that provided benchmarks for the extending surveys in large scales of terrestrial ecosystems.

    Shengnan Yuan, Zhongxin Tan*

    • The adsorption capacity of Cu(II) by C-O-Fe structure biochar is 98.039 mg g1.

    • The biochar skeleton can produce Fe-O–Cu complex with Cu(II).

    • About 49.5% of Cu(II) is immobilized through ion exchange.

    To improve the adsorption effect of biochar on heavy metal Cu(II), we prepared new biochar and explored its modification process influence on original biochar’s physical structure and chemical composition as well as its adsorption mechanism for Cu(II) in an aqueous solution. Through research work, we have reached some significant conclusions: (1) The modified biochar (M2-800) can adsorb Cu(II) at the rate of 98.039 mg g1, 38.8 times higher than that of the original biochar C800 (2.525 mg g1); (2) The biochar modification process boosts its etching and pore expansion, helping Cu(II) enter the inner surface of the adsorbent, but chemical adsorption is still the most essential fixation method for Cu(II); (3) The alkaline modification process promotes the formation of oxygen-containing functional groups, in which-OH/–COOH and iron ions would form C-O-Fe structures such as hydroxyl bridges (Fe-O–) and carboxy bridges (Fe-OOC–); (4) Carboxyl is the primary site of Cu(II) fixation in M2-800, and M2-800 has higher electronegativity (−47.8 mV) and larger pH (11.61), so that Cu(II) can be removed by electrostatic attraction and precipitation.

    Geng Sun, Mei Sun, Zunchang Luo, Chao Li, Xiaoping Xiao, Xiaojing Li, Junjie Zhong, Hua Wang, San’an Nie

    1. Anammox responded to different fertilization practices.

    2. Organic residues treated soils contributed lower (4.07–4.95%) N loss than solely chemical fertilizer (9.13%) in terms of anammox.

    3. Incorporation of organic residues increased the abundance of anammox bacteria but decreased the activity.

    4. The anammox activity was not related to functional gene abundance and soil physicochemical properties.

    The return of crop residue and green manure into agricultural soil is known to be important agricultural management strategies, yet how they affect the anammox process remains poorly characterized. A field experiment containing four treatments: chemical fertilizer (F), F plus rice straw (FS), FS plus green manure (FSM), FSM with integrated management (FSMM), was performed to examine the effects of incorporation of rice straw and green manure residues on anammox. The results showed that the anammox activities in FS and FSM treatments (0.65 and 0.80 nmol N g−1 soil h−1, respectively) were significantly lower than those in F and FSMM treatments (1.60 and 1.28 nmol N g−1 soil h−1, respectively). Anammox contributed 4.07%-4.95% of total N loss in soil incorporated with residues, lower than soil treated with chemical fertilizer only (9.13%), the remaining being due to denitrification. However, the abundance of the hzsB gene (the hydrazine synthase β-subunit gene) in FS and FSM treatments (1.13 × 106 and 1.18 × 106 copies g−1 soil) were significantly higher than soil using chemical fertilizer only (7.49 × 105 copies g−1 soil) while showed no significant difference with FSMM treatment (8.81 × 105 copies g−1 soil). Illumina sequencing indicated that Brocadia was the dominant anammox genus, following by Scalindua and Kuenenia. Anammox bacterial diversity was altered after 4-year incorporation of rice straw and green manure, as shown by α-diversity indices. We concluded that rice straw and green manure incorporated with mineral fertilizer reduce N removal from paddy soil in terms of anammox in spite of stimulating anammox bacterial growth.

    Hao Liu, Yingzhi Ning, Yongqiang Yang, Huaiyin Yang, Li Wang, Lingyun Chen, Yangcuo Wanma, Xiaoya Shen

    • To summarize the utilities of the ecological features based on community structure of the soil ciliates for assessing the ecological restoration quality in grain for green.

    • Revealing the difference in the ciliate community patterns along with the ecological restoration quality of GFG;

    • The soil physical-chemical variables and above-ground plants were the main factors affecting the soil ciliate community composition.

    A 1-year baseline survey was conducted in north-western China to evaluate the ecological restoration quality of grain for green (GFG) using soil ciliate communities. The aims of this study were focused on analyzing the changes of soil ciliate communities in four plots (A, GFG for 15 years; B, GFG for 13 years; C, layland; D, cultivated land) for GFG environmental assessment. Simultaneously we studied the effects of vegetation communities and physical-chemical variables with GFG changes on soil ciliates. A total of 114 species of ciliates were identified among the four sample sites, representing nine classes, 14 orders, 22 families and 37 genera. The community patterns of the soil ciliates were significantly correlated with the individual abundance of aboveground plants, soil water content, and soil porosity. The contents of total nitrogen were the main factor affecting the soil ciliate community composition. The species number, individual abundance, and diversity index of the ciliates was each in the order A>B>C>D; that is, the community composition of ciliates was complicated with the implementation of the GFG. It was shown that succession of ciliate community shift toward promoting the complexity with the progress of GFG. These findings demonstrate that soil ciliate communities may be used as a useful indicator to evaluate the effects of the ecological restoration quality of GFG.

    Irene M. Unger, Robert J. Kremer, Kristen S. Veum, Keith W. Goyne

    • Infestations of Lespedeza cuneata alter soil microbial communities and their actions.

    • Soil alterations persisted up to four years after eradication verses a native prairie.

    • Presence of prairie vegetation may not reflect soil microbial recovery from infestation.

    • Legacy effects of invasives may result in protracted impacts on soil microorganisms.

    • Monitoring soil health indicators in prairies undergoing rehabilitation is important.

    Invasive plant species may alter soil characteristics or interact with the soil microbial community resulting in a competitive advantage. Our objectives were to determine: i) if invasive plant species alter soil properties; and ii) the long-term effects of invasive plant species on soil properties and subsequent implications on ecological restoration efforts. We focused on Lespedeza cuneata, a plant that may be allelopathic. Soil samples were collected from four locations in Central Missouri, USA: an old-field with abundant L. cuneata, two reconstructed sites, and a remnant prairie that has never been plowed. Soil health indictors were used to characterize soil properties at these sites. Nearly every soil property differed significantly between the unplowed prairie reference site and the other three sites. The reconstructed sites, however, generally did not differ from the invaded old-field. These results indicate that the reconstructed prairies are not fully recovered. Although above-ground traits, such as the plant community structure, appear similar to the prairie, the soil microbial community structure still resembles that of an invaded old-field site. These results indicate that more time may be needed before soil microbial populations fully recover after invasive plant removal.