Macroarray analysis of gene transcription during sucrose accumulation in sugar beet (Beta vulgaris L.) root: identification of developmental and metabolism related candidate genes

The presented work integrates molecular data on gene expression with anatomical and biochemical data to analyze the development and the sucrose accumulation process in sugar beet (Beta vulgaris L.) roots. Sugar beet is a biennial Chenopodiacean plant, and it is the major crop for sucrose production in temperate regions. A special root morphology and physiology allow the accumulation of sucrose up to 20% of the fresh weight of the mature root. Approaches to study this storage process at the molecular level have so far been limited to known genes involved in pathways related to sugar metabolism which were mapped and tested for their association with QTLs for sugar yield and quality (Schneider et al., 1999, 2002). In the study presented here, transcription levels in sugar beet roots were analyzed to select candidate genes for the sucrose accumulation process. For this purpose macroarrays were generated from two cDNA collections. The first experiment was performed with 3840 redundant sugar beet cDNAs. A procedure for the analysis including control steps was developed. The performance of the macroarrays was evaluated and compared to commercially produced nylon filters. Both systems could detect transcripts present in as little as 10 copies per cell in agreement with reports by Desprez et al. (1998). Their capacity to analyse transcripts of low abundance was demonstrated in a case study using resistance gene analogues (RGAs). Within an interval of two-fold variation in signal intensities, reproducibility between spots on the same filter was determined to be 98.9%, between spots on different filters 89.8%, and reproducibility after hybridization with two probes synthesized from the same poly(A)+RNA sample was 97.6%. Hybridizations with probes synthesized from different field grown samples of the same organ showed reproducibility for 69.7% of the spots on average. Some precautions were introduced to reduce the sampling effects caused by the variability of environmental conditions. Expression profiles from roots, leaves and inflorescences were generated for 2048 unique cDNAs of the first cDNA clone set. Expression values for each organ were determined by stringent statistical analysis based on eight replica for each clone. Differential expression among the three organs was shown for 917 unique cDNAs, and for 76 unique cDNAs, the amount of detected transcript in roots was at least twice as high as in other organs. For 40 of them a map position was identified and linkage to QTLs is discussed. Additionally, possible functions of preferentially root-expressed candidate genes in taproot morphology and physiology are proposed. As a technical validation, macroarray expression data were confirmed by Northern blot analysis and quantitative RT-PCR experiments. The second set of macroarray experiments was performed with 11520 unique cDNA clones to identify candidate genes in sugar beet roots related to sucrose accumulation or development. For this purpose, a time-course experiment was repeated in two different years. Plants were characterized morphologically and metabolically with respect to their sucrose content during the development. Among the genes differentially expressed in the development, 599 clones with highest expression in the early stages of the first vegetation period were identified in both years. For additional 175 clones, a reproducible preferential expression in the last stages of the development was demonstrated. These candidate genes were classified with respect to their function, and their putative role during development and sucrose accumulation is discussed. Additionally, strategies to focus on the validation of candidates related to sucrose accumulation are discussed. In conclusion, the macroarray technology as established here, together with the selection and characterization of appropriate physiological samples, proved to be a valuable tool to identify new candidate genes related to development and to the sucrose accumulation in the sugar beet root. This is of special importance to sugar beet research because the considered processes cannot be analyzed in model systems without a root storage organ for sucrose

Exploring the loblolly pine (Pinus taeda L.) genome by BAC sequencing and Cot analysis.

Loblolly pine (LP; Pinus taeda L.) is an economically and ecologically important tree in the southeastern U.S. To advance understanding of the loblolly pine (LP; Pinus taeda L.) genome, we sequenced and analyzed 100 BAC clones and performed a Cot analysis. The Cot analysis indicates that the genome is composed of 57, 24, and 10% highly-repetitive, moderately-repetitive, and single/low-copy sequences, respectively (the remaining 9% of the genome is a combination of fold back and damaged DNA). Although single/low-copy DNA only accounts for 10% of the LP genome, the amount of single/low-copy DNA in LP is still 14 times the size of the Arabidopsis genome. Since gene numbers in LP are similar to those in Arabidopsis, much of the single/low-copy DNA of LP would appear to be composed of DNA that is both gene- and repeat-poor. Macroarrays prepared from a LP bacterial artificial chromosome (BAC) library were hybridized with probes designed from cell wall synthesis/wood development cDNAs, and 50 of the "targeted" clones were selected for further analysis. An additional 25 clones were selected because they contained few repeats, while 25 more clones were selected at random. The 100 BAC clones were Sanger sequenced and assembled. Of the targeted BACs, 80% contained all or part of the cDNA used to target them. One targeted BAC was found to contain fungal DNA and was eliminated from further analysis. Combinations of similarity-based and ab initio gene prediction approaches were utilized to identify and characterize potential coding regions in the 99 BACs containing LP DNA. From this analysis, we identified 154 gene models (GMs) representing both putative protein-coding genes and likely pseudogenes. Ten of the GMs (all of which were specifically targeted) had enough support to be classified as intact genes. Interestingly, the 154 GMs had statistically indistinguishable (α = 0.05) distributions in the targeted and random BAC clones (15.18 and 12.61 GM/Mb, respectively), whereas the low-repeat BACs contained significantly fewer GMs (7.08 GM/Mb). However, when GM length was considered, the targeted BACs had a significantly greater percentage of their length in GMs (3.26%) when compared to random (1.63%) and low-repeat (0.62%) BACs. The results of our study provide insight into LP evolution and inform ongoing efforts to produce a reference genome sequence for LP, while characterization of genes involved in cell wall production highlights carbon metabolism pathways that can be leveraged for increasing wood production

Determining the Influence of the Extracellular Proteinase from \u3cem\u3eBrevibacterium linens\u3c/em\u3e on the Metabolism of \u3cem\u3eLactococcus lactis\u3c/em\u3e spp. \u3cem\u3elactis\u3c/em\u3e Using Functional Genomics

Since the catabolism of amino acids in cheese results in the formation of most volatile flavor compounds, a proper intracellular pool of amino acids must be established in order to produce a desirable flavor production in cheese. Generation of this pool of amino acids requires complex interactions among casein and its derivatives, proteolytic enzymes, and transport systems in the associated bacteria, including lactococci. In this project, we hypothesized that casein hydrolysis by the extracellular proteinases of Brevibacterium linens BL2 modulates the expression profile of proteolytic related genes in Lactococcus lactis spp. lactis IL1403. In order to monitor the global gene regulation patterns in L. lactis ssp. lactis IL1403, a high-throughput gene expression tool was needed to study the gene expression profiles on a genomic scale. In this project, we developed a novel oligonucleotide-based filter DNA array protocol for this purpose. The success of this oligonucleotide-based DNA array was dependent on technical innovations including polyI tailing, indirect high density biotin labeling, careful probe design, and integrated computational data analysis. The utility and validity of this protocol were demonstrated by profiling the expression of 375 metabolically related genes in L. lactis ssp. lactis IL1403 during heat, acid, and osmotic stresses. Subsequently the DNA macroarray was used to profile the gene expression changes of L. lactis spp. lactis IL1403 growing in a peptide-limited medium, in a casitone-based peptide-rich medium, and in a casein hydrolyte by B. linens BL2 proteolytic enzymes. L. lactis ssp. lactis IL1403 experienced nitrogen starvation even with an abundance of peptide resources because of lack of expression of peptide transporter genes. Conversely, a peptide pool generated by B. linens BL2 proteolytic activities was sufficient to sustain the growth of L. lactis ssp. lactis IL1403. The repression of the peptide transporter and other peptidase genes of L. lactis ssp. lactis IL1403 was relieved in this medium. Interestingly, the Opt system, a di-tripeptide transporter, was used as a primary peptide transporter, instead of the Opp system whose genes were not actively transcripted in IL1403. We also conducted additional experiments to further describe the protease in B. linens BL2 responsible for the peptide pool generation. This enzyme was secreted as a non-active zymogen and matured into the active protease. Both proteolysis and maturation processes were regulated. Collectively, this work demonstrated that a unique protease of B. linens BL2 generated a pool of pep tides transportable by L. lactis IL1403 and induced changes in gene expression in L. lactis IL1403. Consequently, this body of work demonstrated the hypothesis to be true

ESTs analysis in maize developing kernels exposed to single and combined water and heat stresses

Molecular and metabolic response of plants to a combination of two abiotic stresses is unique and cannot be directly extrapolated from the response of plants to each of the stresses individually. cDNA macroarray has become a useful tool to analyze expression profiles and compare the similarities and differences of various expression patterns. A macroarray of approximately 2,500 maize (Zea mays L.) cDNAs was used for transcriptome profiling in response to single and simultaneous application of water and high temperature stress of maize developing kernels at 15 days after pollination. All stress treatments (water stress-WS, heat stress-HS and their combined application-CS) induced changes in expression of 106 transcripts with 54 up-regulated and 52 down-regulated. There were 11 up-regulated and 15 down-regulated transcripts in common for all three stresses. Although these common transcripts showed existence of a mutual mechanism in stress response, the 23 transcripts induced only in CS indicate that plants responded in a different manner when exposed to simultaneous effects of both stresses. A glimpse of functions regulated under WS, HS and CS is provided, and also the common and different responses between individual and simultaneous stresses.A resposta molecular e metabólica de plantas a uma combinação de dois estresses abióticos é singular, e não pode ser diretamente extrapolada da resposta das plantas a cada um dos estresses individualmente. O macroarranjo do cDNA, tornou-se uma ferramenta útil para analisar os perfís de expressão e comparar as similaridades e diferenças de vários padrões de expressão. Um macroarranjo de 2.500 cDNAs de milho (Zea mays L.) foi usado para traçar um perfil de transcriptoma em resposta ao stress ocasionado por uma única e simultânea aplicação de água e alta temperatura em espigas em desenvolvimento, 15 dias após a polinização. Todos os tratamentos de stress (stress de água - SA, stress de calor - SC e sua aplicação combinada - AC) induziram modificações na expressão de 106 transcritos com 54 regulados acima e 52 regulados abaixo. Houve 11 transcritos regulados acima e 15 regulados abaixo em comum para os três estresses. Embora esses transcritos em comum mostrassem a existência de um mecanismo mútuo na resposta do estresse, os 23 transcritos induzidos somente em AC indicam que as plantas respondem de maneira diferente quando expostos aos efeitos simultâneos de ambos os estresses. Vislumbram-se funções reguladas por SA, SC e AC e também efeitos comuns e diferentes entre estresses individuais e simultâneos

A transcriptomic approach highlights induction of secondary metabolism in citrus fruit in response to Penicillium digitatum infection

<p>Abstract</p> <p>Background</p> <p>Postharvest losses of citrus fruit due to green mold decay, caused by the fungus <it>Penicillium digitaum</it>, have a considerable economic impact. However, little is known about the molecular processes underlying the response of citrus fruit to <it>P. digitatum</it>.</p> <p>Results</p> <p>Here we describe the construction of a subtracted cDNA library enriched in citrus genes preferentially expressed in response to pathogen infection followed by cDNA macroarray hybridization to investigate gene expression during the early stages of colonization of the fruit's peel by <it>P. digitatum</it>. Sequence annotation of clones from the subtracted cDNA library revealed that induction of secondary and amino acid metabolisms constitutes the major response of citrus fruits to <it>P. digitatum </it>infection. Macroarray hybridization analysis was conducted with RNA from either control, wounded, ethylene treated or <it>P. digitatum </it>infected fruit. Results indicate an extensive overlap in the response triggered by the three treatments, but also demonstrated specific patterns of gene expression in response to each stimulus. Collectively our data indicate a significant presence of isoprenoid, alkaloid and phenylpropanoid biosynthetic genes in the transcriptomic response of citrus fruits to <it>P. digitatum </it>infection. About half of the genes that are up-regulated in response to pathogen infection are also induced by ethylene, but many examples of ethylene-independent gene regulation were also found. Two notable examples of this regulation pattern are the genes showing homology to a caffeine synthase and a berberine bridge enzyme, two proteins involved in alkaloid biosynthesis, which are among the most induced genes upon <it>P. digitatum </it>infection but are not responsive to ethylene.</p> <p>Conclusions</p> <p>This study provided the first global picture of the gene expression changes in citrus fruit in response to <it>P. digitatum </it>infection, emphasizing differences and commonalities with those triggered by wounding or exogenous ethylene treatment. Interpretation of the differentially expressed genes revealed that metabolism is redirected to the synthesis of isoprenes, alkaloids and phenylpropanoids.</p

A tiling microarray for global analysis of chloroplast genome expression in cucumber and other plants

Plastids are small organelles equipped with their own genomes (plastomes). Although these organelles are involved in numerous plant metabolic pathways, current knowledge about the transcriptional activity of plastomes is limited. To solve this problem, we constructed a plastid tiling microarray (PlasTi-microarray) consisting of 1629 oligonucleotide probes. The oligonucleotides were designed based on the cucumber chloroplast genomic sequence and targeted both strands of the plastome in a non-contiguous arrangement. Up to 4 specific probes were designed for each gene/exon, and the intergenic regions were covered regularly, with 70-nt intervals. We also developed a protocol for direct chemical labeling and hybridization of as little as 2 micrograms of chloroplast RNA. We used this protocol for profiling the expression of the cucumber chloroplast plastome on the PlasTi-microarray. Owing to the high sequence similarity of plant plastomes, the newly constructed microarray can be used to study plants other than cucumber. Comparative hybridization of chloroplast transcriptomes from cucumber, Arabidopsis, tomato and spinach showed that the PlasTi-microarray is highly versatile

From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma

<p>Abstract</p> <p>Background</p> <p><it>elicobacter pylori </it>infection is associated with several gastro-duodenal inflammatory diseases of various levels of severity. To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach.</p> <p>Results</p> <p>A set of 254 <it>H. pylori </it>genes was used to perform array-based comparative genomic hybridization among 120 French <it>H. pylori </it>strains associated with chronic gastritis (n = 33), duodenal ulcers (n = 27), intestinal metaplasia (n = 17) or gastric extra-nodal marginal zone B-cell MALT lymphoma (n = 43). Hierarchical cluster analyses of the DNA hybridization values allowed us to identify a homogeneous subpopulation of strains that clustered exclusively with <it>cag</it>PAI minus MALT lymphoma isolates. The genome sequence of B38, a representative of this MALT lymphoma strain-cluster, was completed, fully annotated, and compared with the six previously released <it>H. pylori </it>genomes (i.e. J99, 26695, HPAG1, P12, G27 and Shi470). B38 has the smallest <it>H. pylori </it>genome described thus far (1,576,758 base pairs containing 1,528 CDSs); it contains the <it>vacA</it>s2m2 allele and lacks the genes encoding the major virulence factors (absence of <it>cag</it>PAI, <it>bab</it>B, <it>bab</it>C, <it>sab</it>B, and <it>hom</it>B). Comparative genomics led to the identification of very few sequences that are unique to the B38 strain (9 intact CDSs and 7 pseudogenes). Pair-wise genomic synteny comparisons between B38 and the 6 <it>H. pylori </it>sequenced genomes revealed an almost complete co-linearity, never seen before between the genomes of strain Shi470 (a Peruvian isolate) and B38.</p> <p>Conclusion</p> <p>These isolates are deprived of the main <it>H. pylori </it>virulence factors characterized previously, but are nonetheless associated with gastric neoplasia.</p

A streamlined approach to high-throughput proteomics

Proteomics has rapidly become an important tool for life science research, allowing the integrated analysis of global protein expression from a single experiment. To accommodate the complexity and dynamic nature of any proteome, researchers must use a combination of disparate protein biochemistry techniques, often a highly involved and time-consuming process. Whilst highly sophisticated, individual technologies for each step in studying a proteome are available, true high-throughput proteomics that provides a high degree of reproducibility and sensitivity has been difficult to achieve. The development of high-throughput proteomic platforms, encompassing all aspects of proteome analysis and integrated with genomics and bioinformatics technology, therefore represents a crucial step for the advancement of proteomics research. ProteomIQ™ (Proteome Systems) is the first fully integrated, start-to-finish proteomics platform to enter the market. Sample preparation and tracking, centralized data acquisition and instrument control, and direct interfacing with genomics and bioinformatics databases are combined into a single suite of integrated hardware and software tools, facilitating high reproducibility and rapid turnaround times. This review will highlight some features of ProteomIQ, with particular emphasis on the analysis of proteins separated by 2D polyacrylamide gel electrophoresis. © 2005 Future Drugs Ltd

Validation of a commercial allergen microarray platform for specific immunoglobulin E detection of respiratory and plant food allergens

Background: As the use of multiplex-specific immunoglobulin E (sIgE) detection methods becomes increasingly widespread, proper comparative validation assessments of emerging new platforms are vital. Objective: To evaluate the clinical and technical performance of a newly introduced microarray platform, Allergy Explorer (ALEX) (MacroArray Diagnostics), in the diagnosis of pollen (cypress, grass, olive), dust mite (Dermatophagoides pteronyssinus), mold (Alternaria alternata), fruit (apple, peach), and nut (walnut, hazelnut and peanut) allergies and to compare it with those of the ImmunoCAP Immuno Solid-phase Allergen Chip (ISAC) 112 microarray and the ImmunoCAP singleplex method (ThermoFisher Scientific). Methods: We enrolled 153 patients with allergy and 16 controls without atopy. The sIgE assays were conducted using ISAC112, ALEX version 2 (ALEX2), and ImmunoCAP for whole extracts and major components. Technical validation of ALEX2 was performed by measuring repeatability and interassay, interbatch, and interlaboratory reproducibility. Results: When measured globally (detection by 1 or more allergen components), ALEX2 had adequate sensitivity and specificity for most of the allergens studied, comparable in general with that of ISAC112 (except for olive pollen and walnut) and similar to that of ImmunoCAP whole extract measurements. Component-by-component analysis revealed comparable results for all techniques, except for Ole e 1 and Jug r 3, in both ISAC112 and ImmunoCAP comparisons, and Alt a 1, when compared with ISAC112. Continuous sIgE levels correlate with sIgE by ImmunoCAP. Good reproducibility and repeatability were observed for ALEX2.Conclusion: ALEX2 has sound technical performance and adequate diagnostic capacity, comparable in general with that of ISAC112 and ImmunoCAP

Microbial diversity in the municipal composting process and development of detection methods

Composting refers to aerobic degradation of organic material and is one of the main waste treatment methods used in Finland for treating separated organic waste. The composting process allows converting organic waste to a humus-like end product which can be used to increase the organic matter in agricultural soils, in gardening, or in landscaping. Microbes play a key role as degraders during the composting-process, and the microbiology of composting has been studied for decades, but there are still open questions regarding the microbiota in industrial composting processes. It is known that with the traditional, culturing-based methods only a small fraction, below 1%, of the species in a sample is normally detected. In recent years an immense diversity of bacteria, fungi and archaea has been found to occupy many different environments. Therefore the methods of characterising microbes constantly need to be developed further. In this thesis the presence of fungi and bacteria in full-scale and pilot-scale composting processes was characterised with cloning and sequencing. Several clone libraries were constructed and altogether nearly 6000 clones were sequenced. The microbial communities detected in this study were found to differ from the compost microbes observed in previous research with cultivation based methods or with molecular methods from processes of smaller scale, although there were similarities as well. The bacterial diversity was high. Based on the non-parametric coverage estimations, the number of bacterial operational taxonomic units (OTU) in certain stages of composting was over 500. Sequences similar to Lactobacillus and Acetobacteria were frequently detected in the early stages of drum composting. In tunnel stages of composting the bacterial community comprised of Bacillus, Thermoactinomyces, Actinobacteria and Lactobacillus. The fungal diversity was found to be high and phylotypes similar to yeasts were abundantly found in the full-scale drum and tunnel processes. In addition to phylotypes similar to Candida, Pichia and Geotrichum moulds from genus Thermomyces and Penicillium were observed in tunnel stages of composting. Zygomycetes were detected in the pilot-scale composting processes and in the compost piles. In some of the samples there were a few abundant phylotypes present in the clone libraries that masked the rare ones. The rare phylotypes were of interest and a method for collecting them from clone libraries for sequencing was developed. With negative selection of the abundant phylotyps the rare ones were picked from the clone libraries. Thus 41% of the clones in the studied clone libraries were sequenced. Since microbes play a central role in composting and in many other biotechnological processes, rapid methods for characterization of microbial diversity would be of value, both scientifically and commercially. Current methods, however, lack sensitivity and specificity and are therefore under development. Microarrays have been used in microbial ecology for a decade to study the presence or absence of certain microbes of interest in a multiplex manner. The sequence database collected in this thesis was used as basis for probe design and microarray development. The enzyme assisted detection method, ligation-detection-reaction (LDR) based microarray, was adapted for species-level detection of microbes characteristic of each stage of the composting process. With the use of a specially designed control probe it was established that a species specific probe can detect target DNA representing as little as 0.04% of total DNA in a sample. The developed microarray can be used to monitor composting processes or the hygienisation of the compost end product. A large compost microbe sequence dataset was collected and analysed in this thesis. The results provide valuable information on microbial community composition during industrial scale composting processes. The microarray method was developed based on the sequence database collected in this study. The method can be utilised in following the fate of interesting microbes during composting process in an extremely sensitive and specific manner. The platform for the microarray is universal and the method can easily be adapted for studying microbes from environments other than compost.Kompostoinnilla tarkoitetaan biologisesti hajoavan orgaanisen jätteen hajotusta ja se on yksi tärkeimmistä biojätteen käsittelytavoista Suomessa. Mullan kaltaista lopputuotetta voidaan käyttää lannoitteena maataloudessa ja puutarhanhoidossa sekä materiaalina viherrakentamisessa ja maisemoinnissa. Täten jätteenkäsittelymenetelmän ohella kompostointi on myös kierrätysmenetelmä. Kompostointiprosessissa mikrobit ovat tärkeässä roolissa orgaanisen aineen hajottajina. Vaikka kompostoinnin mikrobiologiaa onkin tutkittu jo vuosikymmeniä, mikrobisto teollisessa suuren mittakaavan kompostointilaitoksessa on suurelta osin tuntematon. Tässä väitöskirjatyössä selvitettiin sienten ja bakteerien esiintymistä teollisessa kompostointilaitoksessa ja pienemmässä tutkimuskäyttöön rakennetussa kompostointirummussa molekyylibiologisin menetelmin. Aiemmin on havaittu, että maljakasvatuksiin perustuvilla menetelmillä saadaan selville vain noin 1 % näytteen mikrobiyhteisöstä. Yli 6000 mikrobien tunnistusalueiden DNA-fragmenttia sekvensoitiin ja tuloksena oli yli 500 erilaista bakteerien tunnistussekvenssiä ja 127 erilaista sienten sekvenssiä. Näitä sekvenssejä verrattiin kansainvälisiin sekvenssitietokantoihin. Sekä bakteerien että sienten havaittiin eroavan aiemmissa tutkimuksissa löydetyistä mikrobeista, vaikka yhteneväisyyksiäkin löytyi. Myös aiemmin tunnistamattomia mikrobisekvenssejä oli runsaasti. Tutkimuksessa havaittiin, että mikrobiyhteisöt teollisen- ja tutkimusmittakaavan laitoksella erosivat selvästi. Kloonikirjastoissa on usein monta kappaletta samaa sekvenssiä. Väitöskirjatyössä kehitettiin menetelmä, jolla runsaslukuiset sekvenssit merkitään ennen sekvensointia ja vain harvalukuiset sekvensoidaan. Tällöin tietyt yleiset sekvenssityypit eivät estä harvalukuisempien sekvenssityyppien havainnointia. Menetelmän avulla havaittiin, että 41 % kloonikirjastojen klooneista oli harvinaisia ja vain ne sekvensoitiin. Säästö sekvensoinnissa ja käsiteltävän datan määrässä oli täten huomattava. Kompostin mikrobien esiintymisessä havaittiin eroja prosessin eri vaiheiden välillä. Koska kaikkien mikrobien kloonaaminen ja sekvensointi on aikaa vievää ja kiinnostuksen kohteena on usein vain muutama sekvenssityyppi, kehitettiin näiden sekvenssien havainnointia varten mikrosirudiagnostiikkaan perustuva menetelmä. Mikrosiruja on käytetty lajiston selvittämiseen jo vuosikymmeniä, mutta käytetyt menetelmät ovat olleet puutteellisia herkkyydeltään ja tarkkuudeltaan. Väitöskirjassa kehitetyn mikrosirumenetelmän avulla saavutettiin tarkkuus, jolla kaksi lähisukuista mikrobilajia voitiin erottaa toisistaan. Menetelmä perustuu kahden DNA-koettimen liittämiseen ja työssä suunnitellun kontrollikoettimen käyttöön. Menetelmä osoittautui hyvin herkäksi ja myös pieninä määrinä esiintyvät mikrobit voitiin havainnoida. Mikrosirua voidaan siksi hyödyntää kompostointiprosessin seuraamisessa tai kompostin lopputuotteen hygieenisyyden varmentamisessa. Tämän väitöskirjatyön tulokset tuovat tärkeää tietoa teollisen kompostointiprosessin mikrobiyhteisöstä. Suunniteltua mikrosirumenetelmää voidaan soveltaa myös muiden ympäristöjen mikrobien tutkimiseen