Research Paper Award 2015

Announcement of the M& E Research Paper Award

Based on the results of rigorous review by the selection committee, consisting of the following members, and the final judgment by the Editor-in-Chief, the 2015 “M& E Research Paper Award” was determined as described below.

Selection Committee Members: Satoshi Hanada (Chair, Tokyo Metropolitan Univ.), Hiroyuki Futamata (Shizuoka Univ.), Fumito Maruyama (Kyoto Univ.), Masanori Saito (Tohoku Univ.), Yukari Kuga (Hiroshima Univ.), Kenichi Kucho (Kagoshima Univ.)

Articles Considered for the Award: All original research papers (excluding reviews) published in Microbes and Environments in 2015.

Title and Authors of Research Paper Award article

Burkholderia of Plant-Beneficial Group are Symbiotically Associated with Bordered Plant Bugs (Heteroptera: Pyrrhocoroidea: Largidae).

Takeshita, Kazutaka; Matsuura, Yu; Itoh, Hideomi; Navarro, Ronald; Hori, Tomoyuki; Sone, Teruo; Kamagata, Yoichi; Mergaert, Peter; Kikuchi, Yoshitomo. 30(4): 321–329.

Reasons for Selecting the Research Paper Award Article

This manuscript presents a highly valuable report on gut symbiotic bacteria belonging to the genus Burkholderia in the stinkbug. The authors investigated the gut microbiota in stinkbugs of the Pyrrhocoroid superfamily, which is known to be an ancestor lineage compared to stinkbugs of the Coreoidea or Lygaeoidea superfamily, and discovered that Pyrrhocoroidea stinkbugs harbor a phylogenetically novel group of symbiotic bacteria closely related to the plant-associated beneficial and environmental (PBE) group that is phylogenetically distant from the well-known stinkbug-associated beneficial and environmental (SBE) group in the gut of Coreoidea/Lygaeoidea stinkbugs. This PBE-associated novel Burkholderia clade has been named as “insect-associated PBE (iPBE)” by the authors. By considering the stinkbug phylogeny, their findings strongly suggest that iPBE-type stinkbug symbiotic bacteria were most likely replaced gradually by SBE during the evolution of iPBE-harboring stinkbugs. It should be noted that such a transition of symbiotic bacteria is not limited to just stinkbugs, so that the discovery will have a significant impact on the study of symbiotic bacteria in insects in general. In the present study, not only was the structural analysis of gut symbiotic bacteria conducted but also a wide range of field searching and sampling, histological and anatomical analyses, as well as FISH analysis of symbiotic bacteria. Importantly, the appropriate and effective use of various research methods has made this paper both persuasive and impactful. The meticulous planning and study design that enabled this paper to be highly credible along with the well-organized, easy-to-comprehend structure of the manuscript were also considered, culminating in the honor of the research paper award.

Research Papers Selected by the Committee: a Short List of the Research Paper Award

The following research papers were selected as the top candidates by the six selection committee members. Since these papers were highly appraised for their value and merit by the committee, we are pleased to announce that the following six papers have been selected as “2015 M& E Selection Committee Excellent Research Papers.” Comments from the corresponding committee members for each of these excellent research papers have been provided below.

Futamata‘s choice

Nitrosomonas stercoris sp. nov., a Chemoautotrophic Ammonia-Oxidizing Bacterium Tolerant of High Ammonium Isolated from Composted Cattle Manure.

Nakagawa, Tatsunori; Takahashi, Reiji. 30(3): 221–227.

Comments

By successfully isolating a strain that can grow in conditions having a remarkably high concentration of ammonium (1,000 mM), this paper has initiated a new frontier of research pertaining to microbial ecosystems involved in ammonium removal from environments with high ammonium concentrations. The authors successfully demonstrated the presence and function of microorganisms that adapt to such environments, which are not necessarily extreme but ordinary, exemplifying the profundity of microbial ecology. The authors spent eight years from compost sampling to publication. The name of the newly isolated strain, KYUHI-S (which, in Japanese, sounds very affectionate), is most likely derived from the source of the strain, specifically, composted cattle manure. The diluted compost was cultured in a test tube; however, the unique feature was that it was shaken only for a few seconds over the course of one week, and that subculture was also performed without shaking. This resulted in a conversion of 38 mM NH4+ to 8 mM NO2-. The isolated strain exhibited novel cellular structure. Further ecological analysis including the behavior of such bacteria during composting, genome analysis, and their functional role in nitrogen cycling will be expected in the future.

Maruyama‘s choice

An Efficient Strategy Developed for Next-Generation Sequencing of Endosymbiont Genomes Performed Using Crude DNA Isolated from Host Tissues: A Case Study of Blattabacterium cuenoti Inhabiting the Fat Bodies of Cockroaches.

Kinjo, Yukihiro; Saitoh, Seikoh; Tokuda, Gaku. 30(3): 208–220.

Comments

For various reasons, this study deserves an award for “effort”. The study developed a strategy for effectively determining the draft genome of symbiotic gut bacteria of insects, which is a popular topic of microbial ecology nowadays. Currently, in a variety of environments including deep sea, many initiatives are being undertaken to elucidate cross-talk between the host and its symbiotic bacteria, and a common first step in such studies is to determine the genome of the symbiotic bacteria. However, most of these bacteria are uncultivable, and determining the genome sequence is difficult due to contamination of the host nucleus and mitochondrial genome. Hence, single-cell genomic technologies are being continually advanced when sufficient numbers of cells cannot be obtained. Under such circumstances, rather than attempting to isolate symbiotic bacteria experimentally or developing a new algorithm or methodology, the authors attempted to employ a strategy combining various existing methods to obtain the best result compared to individual existing methods. Although the subject and the objective of this paper are very important from a microbial ecological viewpoint, a quick glance at the paper reveals that the content and charts are unique compared to other papers in M& E. Moreover, given the immenseness of the content, even readers who are unfamiliar with bioinformatics can easily imagine the struggle that might have played out between the authors and the reviewers during the review process. Therefore, in a situation where it might have been natural to opt for the experimental preparation of DNA samples, because DNA sequencing has become significantly less expensive, the tenacious spirit demonstrated by the authors is highly appreciated.

Saito‘s choice

Insecticide-Degrading Burkholderia Symbionts of the Stinkbug Naturally Occupy Various Environments of Sugarcane Fields in a Southeast Island of Japan.

Tago, Kanako; Okubo, Takashi; Itoh, Hideomi; Kikuchi, Yoshitomo; Hori, Tomoyuki; Sato, Yuya; Nagayama, Atsushi; Hayashi, Kentaro; Ikeda, Seishi; Hayatsu, Masahito. 30(1): 29–36.

Comments

This study is based on recent report that uncovered an association of insecticide resistance in stinkbugs with symbiotic bacteria that can degrade the insecticide fenitrothion, and used the sugarcane monoculture fields of Minami Daito Island where the soil and weather conditions are the same but the history of fenitrothion application is different depending upon the fields. The authors analyzed the density of fenitrothion-degrading bacteria in the soil, and the composition and fenitrothion-degrading activity of Burkholderia. The results revealed that the soil and the rhizosphere function as a reservoir for symbiotic bacteria. This paper is highly regarded since it demonstrates that crops, insects, and symbiotic bacteria closely affect each other under the environmental stresses such as pesticide application.

Kuga‘s choice

A New Fractionation and Recovery Method of Viral Genomes Based on Nucleic Acid Composition and Structure Using Tandem Column Chromatography.

Urayama, Syun-ichi; Yoshida-Takashima, Yukari; Yoshida, Mitsuhiro; Tomaru, Yuji; Moriyama, Hiromitsu; Takai, Ken; Nunoura, Takuro. 30(2): 199–203.

Comments

Currently, there is a perceived bias towards viral nucleic acids study due to the lack of comprehensive methods for virus detection. This study proposes a breakthrough technique to simultaneously detect four types of nucleic acids in environmental viruses (dsDNA, ssDNA, dsRNA, and ssRNA) with high efficiency, using hydroxyapatite and cellulose chromatography. Under such circumstances, this study was able to achieve improved yields of viral nucleic acids and simultaneous detection. This promising new technique will likely contribute greatly to advancing virology studies.

Kucho‘s choice

Population Structure of Endomicrobia in Single Host Cells of Termite Gut Flagellates (Trichonympha spp.).

Zheng, Hao; Dietrich, Carsten; Thompson, Claire L.; Meuser, Katja; Brune, Andreas. 30(1): 92–98.

Comments

In recent years, with the increase in next generation sequencing, studies assessing 16S rRNA genes to analyze the community structures of symbiotic bacteria in hosts have become very common. This paper reports a case of triple symbiosis (bacterial symbiosis with flagellates, and flagellate symbiosis with the termite gut). However, the present study stands out in its approach, specifically applying this technique to a single host (flagellate). The authors were successful in obtaining results that were likely anticipated when designing the experimental system, as observed in each of the individual flagellates possessing symbiotic bacteria of only a single lineage, and different species of flagellates possessing symbiotic bacteria of different lineages. Moreover, the discovery of errors that occur when analyzing a tagged library with next-generation sequencing, and highlighting the risk of such errors, will likely advance related studies.

Hanada‘s choice

A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts.

Nilsson, R. Henrik; Tedersoo, Leho; Ryberg, Martin; Kristiansson, Erik; Hartmann, Martin; Unterseher, Martin; Porter, Teresita M.; Bengtsson-Palme, Johan; Walker, Donald M.; de Sousa, Filipe; Gamper, Hannes Andres; Larsson, Ellen; Larsson, Karl-Henrik; Koljalg, Urmas; Edgar, Robert C.; Abarenkov, Kessy. 30(2): 145–150.

Comments

Even though the paper appears ordinary, it is considered as being very useful. Due to the significant spread of next generation DNA sequencing, vast amounts of data are continually being produced; however, the quality of the sequence data has not been sufficiently assessed. To maintain the reliability of the database, modest efforts, as reported in this paper, remain indispensable. The ITS sequence is a ribosomal gene spacer region that is used for the identification of filamentous fungi, and is particularly widely used for species identification. However, chimeric sequences (derived from the mingling of various sequences that have been derived differently) are included in the database, and are known to inhibit identification. This paper reports the detection of chimeric sequences in the database, and has uploaded the identified reference data sets to the UNITE database, which is widely used in studies on fungi. According to the authors, in the existing international database, INSDC, more than 10% of the uploaded ITS sequences are chimeric sequences. It is a pleasure to have such a wonderful paper published in M& E. Moreover, citations of this paper are by far the most among papers that have been published in M& E in 2015, which is indicative of its importance.

to top