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Linking changes in the soil microbial community to C and N dynamics during crop residue decomposition

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Journal of Integrative Agriculture 2021年第11期20卷 3039-3059页

作者： Cyrine REZGUI Isabelle TRINSOUTROT-GATTIN Marie BENOIT Karine LAVAL Wassila RIAH-ANGLET AGHYLE Research Unit UniLaSalleRouen-TeamMont-Saint Aignan 76134France Agroecology and Environment Research Unit IsaraAgroSchool for LifeLyon 69007France

Crop residues are among the main inputs that allow the organic carbon(C)and nutrients to be maintained in agricultural soil.It is an important management strategy that can improve soil fertility and enhance agricultural productivity.This work aims to evaluate the extent of the changes that may occur in the soil heterotrophic microbial communities involved in organic matter decomposition and C and nitrogen(N)mineralization after the addition of crop residues.Soil microcosm experiments were performed at 28℃ for 90 days with the addition of three crop residues with contrasting biochemical qualities:pea(Pisum sativum L.),rapeseed(Brassica napus L.),and wheat(Triticum aestivum L.).Enzyme activities,C and N mineralization,and bacterial and fungal biomasses were monitored,along with the bacterial and fungal community composition,by the highthroughput sequencing of 16 S rRNA and ITS genes.The addition of crop residues caused decreases in β-glucosidase and arylamidase activities and simultaneous enhancement of the C mineralization and net N immobilization,which were linked to changes in the soil microbial communities.The addition of crop residues decreased the bacterial and fungal biomasses 90 days after treatment and there were shifts in bacterial and fungal diversity at the phyla,order,and genera levels.Some specific orders and genera were dependent on crop residue type.For example,Chloroflexales,Inquilinus,Rubricoccus,Clitocybe,and Verticillium were identified in soils with pea residues;whereas Thermoanaerobacterales,Thermacetogenum,and Hypoxylon were enriched in soils with rapeseed residues,and Halanaerobiales,Rubrobacter,and Volutella were only present in soils with wheat residues.The findings of this study suggest that soil C and N dynamics in the presence of the crop residues were driven by the selection of specific bacterial and fungal decomposers linked to the biochemical qualities of the crop residues.If crop residue decomposition processes showed specific bacterial and fungal operational taxonomic unit(OTU)sign

关键词： crop residues C and N mineralization enzyme activities bacterial and fungal diversity

Usefulness of Natural Starters in Food Industry: The Example of Cheeses and Bread

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Food and Nutrition Sciences 2014年第17期5卷 1679-1691页

作者： Demarigny Yann Gerber Pauline BIODYMIA ISARA-Lyon 23 rue Jean Baldassini 69364 Lyon France

Natural starters have been extensively used for many centuries to make many different fermented food products from different raw materials: Milk, meat, roots, vegetables, etc. The industrialisation of food production at the end of the 19th century necessitated the use of regular selected starters to standardize the organoleptic characteristics of the final product. As a consequence, during the 20th century, there was a decline in the use of natural starters in Western countries except in the production of local cheeses or sourdough breads. The beginning of this new millennium has witnessed a deep change in consumer demand, in pursuit of quality, safety and pleasure. In this context, natural starters could, in the future, play an important role in the development of fermented products. However, food producers and researchers have first to cope with fundamental problems in the understanding of these complex ecosystems. The dynamic evolution of the microbial population inside the natural starter (its resilience, its genetic and physiological aptitudes) and the consequences on the product are still partially unknown. This document reviews a broad range of articles concerning the use of natural starters with a specific focus on cheeses and breads, and discusses the major stakes for local food production and the consumption of typical products.

关键词： Natural Starter Cheese Bread Sourdough Food Ecosystem

Utilisation of a Portable Electronic Nose, NeOse Pro, to Follow the Microbial Fermentation of a Yoghurt

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Food and Nutrition Sciences 2021年第1期12卷 90-105页

作者： Yann Demarigny Elodie Legrand Julia Sanchez Arnaud Hallier Nathalie Laurent Sami Slimani Thierry Livache Daniel Picque isara Lyon Equipe AgroLab BioDyMIA (Bioingénierie et Dynamique Microbienne aux Interfaces Alimentaires) ISARA Agrap&#244 le Lyon France Aryballe Technology Grenoble France INRA GMPA AgroParis Tech Paris France

Yoghurt is fermented milk which results from the exclusive action of Lactobacillus delbrueckii subsp bulgaricus and Streptococcus thermophilus. However, a disruption of the bacterial growth can lead to significant industrial losses. Currents monitoring methods, based on the checking of the pH during the fermentation step are not always satisfactory. The NeOse Pro system, a portable electronic nose, is a mean to obtain immediately aromatic profiles. In this work, we applied this technology to the yoghurt ecosystem, a highly hydrated product. The profiles obtained allowed us to discriminate yoghurts before and after fermentation. In detail, the discrepancy between the two bacteria cultured alone was slight. It was also the case when we compared different initial bacterial ratios. However, two different mixes of bacteria led to clearly distinguishable profiles. A GC/MS analysis performed on products fermented 7 h allowed us to explain the detection of acetaldehyde by the stimulation of some captors of the apparatus. NeOse Pro is so convenient to study the fermentation of yogurt.

关键词： NeOse Pro Yoghurt GC/MS Aroma

Spatial analysis of bacteria in brackish lake sediment

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International Journal of Sediment Research 2020年第3期35卷 227-236页

作者： Jean-Sebastien Beaulne Samir R.Mishra Mrutyunjay Suar Ananta Narayan Panda Gurdeep Rastogi Ajit Kumar Pattnaik Vishakha Raina Timothy M.Vogel Environmental Microbial Genomics Ecole Centrale de LyonUniversite de Lyon isara Department of Agroecology and Environment Environmental Biotechnology Laboratory School of BiotechnologyKIIT University Wetland Research and Training Center Chilika Development AuthorityDepartment of Forest and EnvironmentGovernment of Odisha

The spatial distribution of bacterial communities inhabiting sediment is heterogeneous at different spatial scales,but mostly unexplored.Here,it is postulated that the heterogeneity of the bacterial community composition varies at the same scale of the heterogeneity of sediment chemical properties.The large spatial scale(km) diversity in sediment from a brackish water lagoon(Chilika Lake,India) is studied,considering the large scale physical and chemical characteristics of land cover,climate,pH,and salinity.Seventy-two samples(24 stations,3 seasons:winter,rainy,and summer) of sediment from Chilika Lake were analyzed by 16 S ribosomal ribonucleic acid(rRNA) gene sequencing,and the relations with land cover and other physico-chemical paramete rs are discussed.Mo re samples were collected after a severe cyclonic storm(Phailin) passed near the lagoon in 2013,to see the impact of the tropical storm on the spatial and tempo ral distribution of bacteria in the sediment.The results demonstrate clear spatial relations between physico-chemical parameters(e.g.,salinity),land surfaces(e.g.,drainage area),and the distribution of sediment microbial communities.

关键词： Salinity 16S rRNA Macro-scale Sediment GIS

A Rapid Electrophoresis Method on Agarose Gel to Characterise Dairy Protein Aggregates

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Food and Nutrition Sciences 2018年第4期9卷 325-334页

作者： Laetitia Gemelas Pascal Degraeve Marion Morand Arnaud Hallier Yann Demarigny Univ Lyon ISARA Lyon Université Lyon 1 BioDyMIA (Bioingénierie et Dynamique Microbienne aux Interfaces Alimentaires) EA n&#176 3733 ISARA Agrap&#244 le Lyon France Univ Lyon Université Lyon 1 ISARA Lyon BioDyMIA (Bioingénierie et Dynamique Microbienne aux Interfaces Alimentaires) EA n&#176 3733 IUT Lyon 1 technopole Alimentec rue Henri de Boissieu BOURG-EN-BRESSE France General Mills Inc One Global Dairy Vienne Technical Center Chemin des Mines Vienne France isara Lyon Chemistry Laboratory Lyon France

Heat treatment of milk may cause whey proteins and caseins to form aggregates. These soluble and micellar aggregates and their other properties (size, composition, shape, etc.) can affect the techno-functionalities to the milk, conferring interesting or negative features depending on the application in dairy industries. In this study, we propose a new approach to characterise those protein aggregates. SDS-agarose electrophoresis is followed by the calculation of a retention factor (Rf) for each protein spot. Rf allows milk aggregates to be compared qualitatively under the same conditions. This method could be transposed to the dairy industry for a better knowledge of the milk subsequent to heat treatment.

关键词： Heat Treatment of Milk Dairy Protein Aggregates Agarose Gel Electrophoresis

The Citrate Metabolism in Homo-and Heterofermentative LAB:A Selective Means of Becoming Dominant over Other Microorganisms in Complex Ecosystems

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Food and Nutrition Sciences 2014年第10期5卷 953-969页

作者： Gemelas Laetitia Degraeve Pascal Demarigny Yann isara-Lyon AgrapoleFood Microbiology LaboratoryBIODYMIALyonFrance Lyon 1 University Research Laboratory in Industrial Engineering Food—BIODYMIA EA 373Bourg-en-BresseFrance

The citrate metabolism has been extensively studied in lactic acid bacteria (LAB) for its aroma compound production. Among the 4-carbon (C4) by-products obtained from citrate fermentation, diacetyl is one of the better known products for its contribution to the buttery aroma of dairy products. A lot of documents deal with ways to improve diacetyl concentration in food matrices. Apart from these organoleptic advantages, in a microbial ecosystem, the citrate metabolism gives selective advantages to citrate positive microorganisms. Citrate metabolism allows the LAB to use another carbon source for their growth, withstand acidic conditions and generate a “proton motive force” (PMF). Moreover, the citrate/glucid co-metabolism leads to the fast release of organic compounds known for having bacteriostatic effects. Under specific conditions, the C4?pathway liberates diacetyl which is bacteriostatic. In this review we first describe the citrate metabolism and the enzymes involved in the two homo- and heterofermentative LABLc diacetylactisandLeuconostocspp. Moreover, the way to shift the metabolic pathway toward the production of aromatic compounds is discussed for both of these fermentative types of bacteria. Finally, the selective advantages of citrate metabolism for LAB in complex microbial ecosystems are delineated.

关键词： Citrate Metabolism Lactococcus lactis subsp.lactis biovar.diacetylactis Leuconostoc spp. Complex Microbial Ecosystems Homo-and Heterofermentative Lactic Acid Bacteria

Agronomic assessment of two populations of intermediate wheatgrass—Kernza^(®)(Thinopyrum intermedium)in temperate South America

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Grassland Research 2022年第4期1卷 262-278页

作者： Andres Locatelli Lucia Gutierrez Olivier Duchene Pablo R.Speranza Valentin D.Picasso Risso Polo agro-alimentario Centro Universitario Litoral NorteEstacion Experimental Mario Antonio CassinoniUniversidad de la RepúblicaPaysanduUruguay Departamento de Producción Vegetal Facultad de AgronomiaUniversidad de la RepúblicaPaysanduUruguay Departamento de Biometría Estadística y ComputaciónFacultad de AgronomíaUniversidad de la RepúblicaMontevideoUruguay Department of Agronomy University of Wisconsin–MadisonMadisonWisconsinUSA Agroecology and Environment Research Unit ISARALyonFrance Departamento de Biología Vegetal Facultad de AgronomiaUniversidad de la RepúblicaMontevideoUruguay Departamento de Producción Animal y Pasturas Facultad de AgronomiaUniversidad de la RepúblicaMontevideoUruguay

Background Kernza®intermediate wheatgrass is a perennial grain and forage crop that can provide several ecosystem services.Major research efforts focused on Kernza have taken place in high latitudes.The goal of this study was to evaluate,for the first time,the agronomic performance of Kernza in a low-latitude region with mild winters.Methods A KS-cycle 4 Kernza population(A)was planted in spring in Wisconsin,USA,and selected in one cycle for lower vernalization requirements,obtaining a new population(B).These two populations,at three nitrogen(N)fertilization rates,were evaluated in a full factorial,completely randomized field experiment in Uruguay over 2 years.Results The populations were similar in grain yields and flowering time in the 1st year,but population B had 63%lower grain yield in the 2nd year and 20%lower forage yield throughout the experiment.Increasing the N rate to 160 kg ha−1 led to a 63%increase in grain yield and 28%increase in forage yield across populations.Forage yields and nutritive values were similar to those reported in the northern hemisphere.However,grain yields for both the 1st(316 kg ha−1)and 2nd year(41 kg ha−1)were lower due to reduced flowering and weed competition.Conclusions Expansion of Kernza to lower-latitude regions will require further breeding to improve reproductive performance.

关键词： low-latitude regions nitrogen fertilization rates perennial grains Thinopyrum intermedium vernalization requirements

The Use of Appropriate Communication Channels to Understand Life Threatening Diseases: A Study of Viral Hepatitis Infection among Onikolobo Residents in Abeokuta, Nigeria

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Advances in Infectious Diseases 2015年第4期5卷 189-195页

作者： Amos Kolawole Amoo John Kehinde Adegboyega Taofeek Tope Agu Georgia Chinemenwa Tejuosho Wasiu Department of Mass Communication Moshood Abiola Polytechnic Abeokuta Nigeria State Hospital Isara Nigeria Department of Biological Sciences Southwestern University Nigeria Ijebu Nigeria Department of Microbiology Olabisi Onabanjo University Ago-Iwoye Nigeria

This work examines the use of communication channels to sensitize the people about life threatening diseases with special emphasis on Hepatitis. It becomes very topical at this moment because most of the viral infections wreak havoc such as Acquired Immune Deficiency Syndrome (AIDS) and more recently, Ebola Virus Disease (EVD) assumed an epidemic proportion because the people were not adequately sensitized with precautionary measures against them. One of such measures is dissemination of useful information on how to avoid or contain such viral infections. It also concerns itself with hepatitis because of its contagious nature and the way it attacks the liver. The study reviews relevant concepts to information dissemination. It discovers that as deadly as the disease is, most people, including some health attendants in hospitals do not understand what it means and how it is contracted. In addition, it was discovered that 60% of the total respondents did not know about hepatitis. 73% of those who claimed they knew about it knew through friends and not through the media. 80% of those who claimed they sought health information from the media did not know about hepatitis. 65% of those who claimed they had high access to radio did not really seek health information from the radio. In the communities in Nigeria, we suggest that there should be increased public awareness about viral diseases, complete immunization against viral hepatitis and better sanitation facilities. Other efforts by the Government should include the provision of safe drinking water;expansion of well-equipped hospitals among other health developmental programmes will go a long way in the reduction of hepatitis in communities, among pregnant women as well as its associated maternal effects in the communities.

关键词： Communication Hepatitis Onikolobo Abeokuta Nigeria

Influence of the Backslopping Practice on the Microbial Diversity of the Lactococcus Population in a Model Cheesemaking

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Food and Nutrition Sciences 2011年第6期2卷 618-627页

作者： Yann Demarigny Marion Dalmasso Aline Tonleu Véronique Rigobello Eric Beuvier Mai Huong Ly-Chatain Yvette Bouton isara-Lyon AgrapoleLaboratoire de microbiologie alimentaireLyonFrance INRA-UR342 Technologie et Analyses Laitières PolignyFrance ComitéInterprofessionnel du Gruyère de Comté R&D Unit PolignyFrance

The objective of this work was to study the microbial diversity of natural whey starters (NWS), with a special focus on Lactococcus strains, during 10 successive days of backslopping. Each day, whey samples were enumerated for their Lactococcus, Enterococcus, Leuconostoc and Lactobacillus levels. The diversity and dynamics of the Lactococcus population in whey were investigated using phenotypic methods such as acidifying aptitude and enzymatic activities. Molecular approach using REP-PCR, ERIC-PCR, plamid profiles, phages and prophages research and PFGE was also applied. Lactococci were the main population in whey. Strains from raw milk were sub-dominant. Based on PFGE and phenotypic results lactococci in whey displayed a more heterogeneous phenotype and pulsotype which may reflect greater variations than previously observed within starter. No phages and prophages were spotted on. Plasmids did not seem to be exchanged from strain to strain. The backslopping practice seemed to allow the strains of the starter to rapidly acquire a specificity of their own. The changes observed presumed a slow adaptation of the strains to the “back- slopping environment”. The study of NWS diversity constitutes an important step for the comprehension of acidification defects that recurrently occur in cheesemaking technologies using the backslopping practice.

关键词： Backslopping Natural Whey Starter Model Cheesemaking Lactococcus