Soil amendment with biochar is evaluated globally as a means to improve soil fertility and to mitigate climate change. However, the effects of biochar on soil biota have received much less attention than its effects on soil chemical properties. A review of the literature reveals a significant number of early studies on biochar-type materials as soil amendments either for managing pathogens, as inoculant carriers or for manipulative experiments to sorb signaling compounds or toxins. However, no studies exist in the soil biologyliterature that recognize the observed largevariations ofbiochar physico-chemical properties. This shortcoming has hampered insight into mechanisms by which biochar influences soil microorganisms, fauna and plant roots. Additional factors limiting meaningful interpretation of many datasets are the clearly demonstrated sorption properties that interfere with standard extraction procedures for soil microbial biomass or enzyme assays, and the confounding effects of varying amounts of minerals. In most studies, microbial biomass has been found to increase as a result of biochar additions, with significant changes in microbial community composition and enzyme activities that may explain biogeochemical effects of biochar on element cycles, plant pathogens, and crop growth. Yet, very little is known about the mechanisms through which biochar affects microbial abundance and community composition. The effects of biochar on soil fauna are even less understood than its effects on microorganisms, apart from several notable studies on earthworms. It is clear, however, that sorption phenomena, pH and physical properties of biochars such as pore structure, surface area and mineral matter play important roles in determining how different biochars affect soil biota. Observations on microbial dynamics lead to the conclusion of a possible improved resource use due to co-location of various resources in and around biochars. Sorption and therebyinactivation of growth-inhibiting substances likelyplaysa rolefor increased abundance of soil biota. No evidence exists so far for direct negative effects of biochars on plant roots. Occasionally observed decreases in abundance of mycorrhizal fungi are likely caused by concomitant increases in nutrient availability,reducing theneedfor symbionts.Inthe shortterm,therelease ofavarietyoforganic molecules from fresh biochar may in some cases be responsible for increases or decreases in abundance and activity of soil biota. A road map for future biochar research must include a systematic appreciation of different biochar-types and basic manipulative experiments that unambiguously identify the interactions between biochar and soil biota.

http://www.css.cornell.edu/faculty/lehmann/pictures/publ/SoilBiolBiochem%2043,%201812–1836,%202011%20Lehmann.pdf

Biochar effects on soil biota – A review

Gene families are growing rapidly, but standard methods for inferring phylogenies do not scale to alignments with over 10,000 sequences. We present FastTree, a method for constructing large phylogenies and for estimating their reliability. Instead of storing a distance matrix, FastTree stores sequence profiles of internal nodes in the tree. FastTree uses these profiles to implement neighbor-joining and uses heuristics to quickly identify candidate joins. FastTree then uses nearest-neighbor interchanges to reduce the length of the tree. For an alignment with N sequences, L sites, and a different characters, a distance matrix requires O(N^2) space and O(N^2 L) time, but FastTree requires just O( NLa + N sqrt(N) ) memory and O( N sqrt(N) log(N) L a ) time. To estimate the tree's reliability, FastTree uses local bootstrapping, which gives another 100-fold speedup over a distance matrix. For example, FastTree computed a tree and support values for 158,022 distinct 16S ribosomal RNAs in 17 hours and 2.4 gigabytes of memory. Just computing pairwise Jukes-Cantor distances and storing them, without inferring a tree or bootstrapping, would require 17 hours and 50 gigabytes of memory. In simulations, FastTree was slightly more accurate than neighbor joining, BIONJ, or FastME; on genuine alignments, FastTree's topologies had higher likelihoods. FastTree is available at http://microbesonline.org/fasttree.

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Fast Tree: Computing Large Minimum-Evolution Trees with Profiles instead of a Distance Matrix

Nitrogen is an essential component of all living organisms and the main nutrient limiting life on our planet By far, the largest inventory of freely accessible nitrogen is atmospheric dinitrogen, but most organisms rely on more bioavailable forms of nitrogen, such as ammonium and nitrate, for growth The availability of these substrates depends on diverse nitrogen-transforming reactions that are carried out by complex networks of metabolically versatile microorganisms In this Review, we summarize our current understanding of the microbial nitrogen-cycling network, including novel processes, their underlying biochemical pathways, the involved microorganisms, their environmental importance and industrial applications

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The microbial nitrogen-cycling network

B6nassy, C., 1955. R6marques sur deux Aphelinid6s: Aphelinus mytilaspidis Le Baron et Aphytis proclia Walker. Annls l~piphyt. 6: 11-17. Lord, F. T. & MacPhee, A. W., 1953. The influence of spray programs on the fauna of apple orchards in Nova Scotia II. Oyster shell scale. Can. Ent. 79: 196-209. Pickett, A. D., 1946. A progress report on long term spray programs. Rep. Nova Scotia Fruit Grow. Ass. 83 : 27-31. Pickett, A. D., 1967. The influence of spray programs on the fauna of apple orchards in Nova Scotia XIV. Can. Ent. 97: 816-821. Tothill, J. D., 1918. The predacious mite Hemisarcoptes malus Shimer and its relation to the natural control of the oyster shell scale Lepidosaphes ulmi L. Agric. Gaz. Can. 5 : 234-239.

http://link.springer.com/content/pdf/10.1007/BF01976688.pdf

Soil enzymes: Kuprevich, V. F. & Shcherbakova, T. A.: Translated from the Russian edition (1966), published by the Indian National Scientific Documentation Centre, New Delhi 1971. 392 pp., offset printing from type script, paper cover. Obtainable from U.S. Department of Commerce, National Technical Information Service, Springfield, Va. 22151

Biological dinitrogen (N2) fixation is a natural process of significant importance in world agriculture. The demand for accurate determinations of global inputs of biologically-fixed nitrogen (N) is strong and will continue to be fuelled by the need to understand and effectively manage the global N cycle. In this paper we review and update long-standing and more recent estimates of biological N2 fixation for the different agricultural systems, including the extensive, uncultivated tropical savannas used for grazing. Our methodology was to combine data on the areas and yields of legumes and cereals from the Food and Agriculture Organization (FAO) database on world agricultural production (FAOSTAT) with published and unpublished data on N2 fixation. As the FAO lists grain legumes only, and not forage, fodder and green manure legumes, other literature was accessed to obtain approximate estimates in these cases. Below-ground plant N was factored into the estimations. The most important N2-fixing agents in agricultural systems are the symbiotic associations between crop and forage/fodder legumes and rhizobia. Annual inputs of fixed N are calculated to be 2.95 Tg for the pulses and 18.5 Tg for the oilseed legumes. Soybean (Glycine max) is the dominant crop legume, representing 50% of the global crop legume area and 68% of global production. We calculate soybean to fix 16.4 Tg N annually, representing 77% of the N fixed by the crop legumes. Annual N2 fixation by soybean in the U.S., Brazil and Argentina is calculated at 5.7, 4.6 and 3.4 Tg, respectively. Accurately estimating global N2 fixation for the symbioses of the forage and fodder legumes is challenging because statistics on the areas and productivity of these legumes are almost impossible to obtain. The uncertainty increases as we move to the other agricultural-production systems—rice (Oryza sativa), sugar cane (Saccharum spp.), cereal and oilseed (non-legume) crop lands and extensive, grazed savannas. Nonetheless, the estimates of annual N2 fixation inputs are 12–25 Tg (pasture and fodder legumes), 5 Tg (rice), 0.5 Tg (sugar cane), <4 Tg (non-legume crop lands) and <14 Tg (extensive savannas). Aggregating these individual estimates provides an overall estimate of 50–70 Tg N fixed biologically in agricultural systems. The uncertainty of this range would be reduced with the publication of more accurate statistics on areas and productivity of forage and fodder legumes and the publication of many more estimates of N2 fixation, particularly in the cereal, oilseed and non-legume crop lands and extensive tropical savannas used for grazing.

Global inputs of biological nitrogen fixation in agricultural systems

Nitrogen is generally the most limiting nutrient for rice production. In rice paddy soils, various biochemical processes can occur regarding N cycling, including nitrification, denitrification, and nitrogen fixation. Since its discovery in the 1930s, the nitrification-denitrification process has been extensively studied in Japan. It may cause N loss from rice paddy soils, while it can also reduce environmental pollutions such as nitrate leaching and emission of nitrous oxide (N2O). In this review article, we first summarize the early and important findings regarding nitrification-denitrification in rice paddy soils, and then update recent findings regarding key players in denitrification and N2O reduction. In addition, we also discuss the potential occurrence of other newly found reactions in the N cycle, such as archaeal ammonia oxidization, fungal denitrification, anaerobic methane oxidation coupled with denitrification, and anaerobic ammonium oxidation.

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Nitrogen Cycling in Rice Paddy Environments: Past Achievements and Future Challenges

Denitrification is an important part of the nitrogen cycle in the environment, and diverse bacteria, archaea, and fungi are known to have denitrifying ability. Rice paddy field soils have been known to have strong denitrifying activity, but the microbes responsible for denitrification in rice paddy field soils are not well known. Present study analyzed the diversity and quantity of the nitrite reductase genes (nirS and nirK) in a rice paddy field soil, sampled four times in one rice-growing season. Clone library analyses suggested that the denitrifier community composition varied over sampling time. Although many clones were distantly related to the known NirS or NirK, some clones were related to the NirS from Burkholderiales and Rhodocyclales bacteria, and some were related to the NirK from Rhizobiales bacteria. These denitrifiers may play an important role in denitrification in the rice paddy field soil. The quantitative PCR results showed that nirK was more abundant than nirS in all soil samples, but the nirK/nirS ratio decreased after water logging. These results suggest that both diversity and quantity changed over time in the rice paddy field soil, in response to the soil condition.

Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

Denitrification is an important process in the global nitrogen cycle. The genes encoding NirK and NirS (nirK and nirS), which catalyze the reduction of nitrite to nitric oxide, have been used as marker genes to study the ecological behavior of denitrifiers in environments. However, conventional polymerase chain reaction (PCR) primers can only detect a limited range of the phylogenetically diverse nirK and nirS. Thus, we developed new PCR primers covering the diverse nirK and nirS. Clone library and qPCR analysis using the primers showed that nirK and nirS in terrestrial environments are more phylogenetically diverse and 2–6 times more abundant than those revealed with the conventional primers. RNA- and culture-based analyses using a cropland soil also suggested that microorganisms with previously unconsidered nirK or nirS are responsible for denitrification in the soil. PCR techniques still have a greater capacity for the deep analysis of target genes than PCR-independent methods including metagenome analysis, although efforts are needed to minimize the PCR biases. The methodology and the insights obtained here should allow us to achieve a more precise understanding of the ecological behavior of denitrifiers and facilitate more precise estimate of denitrification in environments.

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Higher diversity and abundance of denitrifying microorganisms in environments than considered previously.

We succeeded in isolating an aerobic bacterium, which utilizes γ-HCH as a sole carbon source and can rapidly and completely decompose this substance. This bacterium was isolated from a γ-HCH plot of a long-term experimental upland field where the applied γ-HCH disappeared rapidly within I month. The bacterium was identified as Pseudomonas paucimobilis. It was suggested that the rapid loss of the applied γ-HCH in the upland field was closely related to the presence of the bacterium. In addition, P. paucimobilis had the ability to decompose the applied γ-HCH even in other soils where γ-HCH had never been applied. The pathway of γ-HCH decomposition by P. paucimobilis was found to be rather exceptional in that some chlorophenols were identified as the intermediate products of γ-HCH decomposition.

https://www.tandfonline.com/doi/pdf/10.1080/00380768.1989.10434739

Isolation and identification of an aerobic γ-HCH-decomposing bacterium from soil

Various single-cell isolation techniques, including dilution, micromanipulation, flow cytometry, microfluidics, and compartmentalization, have been developed. These techniques can be used to cultivate previously uncultured microbes, to assess and monitor cell physiology and function, and to screen for novel microbiological products. Various other techniques, such as viable staining, in situ hybridization, and those using autofluorescence proteins, are frequently combined with these single-cell isolation techniques depending on the purpose of the study. In this review article, we summarize currently available single-cell isolation techniques and their applications, when used in combination with other techniques, in microbiological and biotechnological studies.

Keishi Senoo

Papers

Nitrogen Cycling in Rice Paddy Environments: Past Achievements and Future Challenges

Temporal shifts in diversity and quantity of nirS and nirK in a rice paddy field soil

Higher diversity and abundance of denitrifying microorganisms in environments than considered previously.

Isolation and identification of an aerobic γ-HCH-decomposing bacterium from soil

Single-cell analysis and isolation for microbiology and biotechnology: methods and applications.