Ecosystem services of soil microbial communities - developing sustainable cultivation methods for agriculture

The aim of the project is to develop innovative and feasible agro-environmental technology for improvement of environmental sustainability of cultivation methods. This will be achieved by increasing soil crop cover taking advantage of ecosystem services of soil microbes to suppress crop pathogens as an alternative system for chemical control, and to optimal degradation of crop residues

Stable carbon isotope fractionation during methanogenesis in three boreal peatland ecosystems

The degradation of organic matter to CH4 and CO2 was investigated in three different boreal peatland sys- tems in Finland, a mesotrophic fen (MES), an oligotrophic fen (OLI), and an ombrotrophic peat (OMB). MES had sim- ilar production rates of CO2 and CH4, but the two nutrient- poor peatlands (OLI and OMB) produced in general more CO2 than CH4. δ 13C analysis of CH4 and CO2 in the pres- ence and absence methyl fluoride (CH3F), an inhibitor of acetoclastic methanogenesis, showed that CH4 was predom- inantly produced by hydrogenotrophic methanogenesis and that acetoclastic methanogenesis only played an important role in MES. These results, together with our observations concerning the collective inhibition of CH4 and CO2 pro- duction rates by CH3F, indicate that organic matter was de- graded through different paths in the mesotrophic and the nutrient-poor peatlands. In the mesotrophic fen, the ma- jor process is canonical fermentation followed by aceto- clastic and hydrogenotrophic methanogenesis, while in the nutrient-poor peat, organic matter was apparently degraded to a large extent by a different path which finally involved hydrogenotrophic methanogenesis. Our data suggest that degradation of organic substances in the oligotrophic envi- ronments was incomplete and involved the use of organic compounds as oxidants.Peer reviewe

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos

Development and Deployment of High-Throughput Retrotransposon-Based Markers Reveal Genetic Diversity and Population Structure of Asian Bamboo

Bamboo, a non-timber grass species, known for exceptionally fast growth is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo, contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Due to their random insertion behavior, interspaces of retrotransposons can vary significantly among bamboo genotypes. Capitalizing this feature, inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there are no transposon based markers reported from the bamboo genome and particularly using IRAP markers on genetic diversity. Phyllostachys genus of Asian bamboo is the largest of the Bambusoideae subfamily, with great economic importance. We report structure-based analysis of bamboo genome for the LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, which revealed a total of 98,850 retrotransposons with intact LTR sequences at both the ends. Grouped into 64,281 clusters/scaffold using CD-HIT-EST software, only 13 clusters of retroelements were found with more than 30 LTR sequences and with at least one copy having all intact protein domains such as gag and polyprotein. A total of 16 IRAP primers were synthesized, based on the high copy numbers of conserved LTR sequences. A study using these IRAP markers on genetic diversity and population structure of 58 Asian bamboo accessions belonging to the genus Phyllostachys revealed 3340 amplicons with an average of 98% polymorphism. The bamboo accessions were collected from nine different provinces of China, as well as from Italy and America. A three phased approach using hierarchical clustering, principal components and a model based population structure divided the bamboo accessions into four sub-populations, PhSP1, PhSP2, PhSP3 and PhSP4. All the three analyses produced significant sub-population wise consensus. Further, all the sub-populations revealed admixture of alleles. The analysis of molecular variance (AMOVA) among the sub-populations revealed high intra-population genetic variation (75%) than inter-population. The results suggest that Phyllostachys bamboos are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the usability of IRAP markers in determining the inter-species variability of Asian bamboos

Development and deployment of high-throughput retrotransposon-based markers reveal genetic diversity and population structure of Asian bamboo

Bamboo, a non-timber grass species, known for exceptionally fast growth, is a commercially viable crop. Long terminal repeat (LTR) retrotransposons, the main class I mobile genetic elements in plant genomes, are highly abundant (46%) in bamboo contributing to genome diversity. They play significant roles in the regulation of gene expression, chromosome size and structure as well as in genome integrity. Inter-retrotransposon amplified polymorphism (IRAP) is a high-throughput method to study the genetic diversity of plant species. Till date, there are no markers based on Transposable Elements (TEs) for the bamboo genome and no reports on bamboo genetic diversity using the IRAP method. Phyllostachys is an Asian bamboo, the largest group in the bamboo subfamily, Bambusoideae, and it is of great economic value due to its fast growth. The structure of LTR-retrotransposon superfamilies, Ty3-gypsy and Ty1-copia, were analysed in the bamboo genome using LTRharvest and LTRdigest software. A total of 98,850 LTR retrotransposons with both ends of intact LTR sequences were identified, grouped into 64,281 clusters/scaffolds, using CD-HIT software. Among the total of 64,281 clusters, 13 clusters had more than 30 copy numbers of LTR sequences and at least one copy had all intact protein domains such as gag protein and polyprotein. Based on the high copy numbers of conserved LTR sequences, a total of 16 IRAP primers were developed. All these IRAP primers were used to study the genetic diversity and population structure of the Asian bamboo. AMOVA analysis was done for 58 Asian bamboo species collected from nine different provinces of China, from Italy and America. In the bamboo species, these IRAP primers produced a total of 3340 amplicons with an average of 98% polymorphism. The 58 Asian bamboo species were grouped into two major clusters and four sub-clusters, based on UPGMA analysis. UPGMA cluster analysis was corroborated by statistical analyses of genetic similarity coefficients. Structure analysis showed that the bamboo species could be divided into four subpopulations (K = 4): SP1, SP2, SP3 and SP4. All SPs had an admixture of alleles. AMOVA analysis showed that higher genetic variations occurred within populations (75%) rather than among populations (25%). The study highlights the usability of IRAP in Asian bamboo to determine inter-species variability using retrotransposon markers.Peer reviewe

Pellon kasvipeitteisyyden teknologia muuttuvassa ilmastossa – maaperämikrobien ekosysteemipalvelujen hyödyntäminen

Maatalous kohtaa ilmastonmuutoksen myötä entistä suurempia ympäristöhaasteita. Eroosio– jaravinnekuorma vesistöihin kasvaa, mikäli talvet muuttuvat ennustetulla tavalla lauhemmiksi jasateisemmiksi. Talviaikainen kasvipeitteisyys suojaa maan pintaa vähentäen eroosio– jaravinnehuuhtoumariskiä. Kevätkylvöisten kasvien viljelyssä kasvukauden ulkopuolinenkasvipeitteisyys voidaan toteuttaa sekä vähentämällä syysmuokkausta (mm. kevennetty muokkaus,suorakylvö sänkeen keväällä) että lisäämällä viljelykiertoon monivuotisia kasveja. Muokkaustakevennettäessä edellisen vuoden kasvustojäte voi hidastaa maan lämpenemistä ja kuivumista keväällä,sekä luoda suotuisat olosuhteet maa– jakasvinjätelevintäisille kasvitaudeille. Kasvipeitteisyydenympäristöhyöty vähenee, mikäli torjuntaaineidenkäyttötarve lisääntyy.Peltomaassa on yleensä jossain määrin luontaista kykyä estää taudinaiheuttajien kehittymistä jakasvua. Syynä ovat muut maaperän mikrobit: tietyt maaperämikrobit voivat tuottaa toisten mikrobienkasvua estäviä ns. antagonistisia yhdisteitä ja mikrobiston monimuotoisuuden sinänsä on todettuvahvistavan maan kykyä tukahduttaa sienitauteja. Maaperän mikrobiston koostumuksen ratkaisevanatekijänä on viljelytekniikka, joka vaikuttaa maamikrobien ravintoon ja elinympäristön olosuhteisiin.Tällaisia viljelyteknisiä keinoja ovat mm. maan muokkaus ja viljelykierto.Vuonna 2009 aloitettiin hanke ’Tuotannon kestävyys muuttuvissa ilmastooloissa– teknologisetratkaisut ja maaperäbiologisten ekosysteemipalvelujen hyödyntäminen’, jonka tavoitteena on kehittääinnovatiivistä ja käytännön peltoviljelyyn soveltuvaa maatalouden ympäristöteknologiaa peltojenkasvipeitteisyyden lisäämiseksi samalla hyödyntäen maaperämikrobiston ekosysteemipalvelujatautimikrobien tukahduttamiseksi luontaisin menetelmin ja kasvijätteen toivotunlaiseksi hajotukseksi.Hankkeessa on monitieteinen tutkimusryhmä MTT:n ja Helsingin yliopiston tutkijoita maataloudenympäristöteknologiasta, ympäristöbiotekniikasta, biologiasta ja mikrobiologiasta.Posterissa annetaan yleiskuva hankkeesta (ks. myös posteri Knuutila ym.) sekä esitellääntarkemmin kasvitautien luontaiseen tukahduttamiseen eli tautisuppressiivisuuteen keskittyvääosahanketta

Genetics and genomics of moso bamboo (Phyllostachys edulis) : Current status, future challenges, and biotechnological opportunities toward a sustainable bamboo industry

Sustainable goals for contemporary world seek viable solutions for interconnected challenges, particularly in the fields of food and energy security and climate change. We present bamboo, one of the versatile plant species on earth, as an ideal candidate for bioeconomy for meeting some of these challenges. With its potential realized, particularly in the industrial sector, countries such as China are going extensive with bamboo development and cultivation to support a myriad of industrial uses. These include timber, fiber, biofuel, paper, food, and medicinal industries. Bamboo is an ecologically viable choice, having better adaptation to wider environments than do other grasses, and can help to restore degraded lands and mitigate climate change. Bamboo, as a crop species, has not become amenable to genetic improvement, due to its long breeding cycle, perennial nature, and monocarpic behavior. One of the commonly used species, moso bamboo (Phyllostachys edulis) is a potential candidate that qualifies as industrial bamboo. With its whole-genome information released, genetic manipulations of moso bamboo offer tremendous potential to meet the industrial expectations either in quality or in quantity. Further, bamboo cultivation can expect several natural hindrances through biotic and abiotic stresses, which needs viable solutions such as genetic resistance. Taking a pragmatic view of these future requirements, we have compiled the present status of bamboo physiology, genetics, genomics, and biotechnology, particularly of moso bamboo, to drive various implications in meeting industrial and cultivation requirements. We also discuss challenges underway, caveats, and contextual opportunities concerning sustainable development.Peer reviewe

Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element

Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene therapy. Two active MLEs, Ppmar1 and Ppmar2, have previously been identified in moso bamboo (Phyllostachys edulis). Both of these have a preferential insertion affinity to AT-rich region and their insertion sites are close to random in the host genome. In Ppmar2 element, we studied the affinities of terminal inverted repeats (TIRs) to DNA binding domain (DBD) and their influence on the transposition activity. We could identify two putative boxes in the TIRs which play a significant role in defining the TIR’s affinities to the DBD. Seven mutated TIRs were constructed, differing in affinities based on similarities with those of other plant MLEs. Gel mobility shift assays showed that the TIR mutants with mutation sites G669A-C671A had significantly higher affinities than the mutants with mutation sites C657T-A660T. The high-affinity TIRs indicated that their transposition frequency was 1.5–2.0 times higher than that of the wild type TIRs in yeast transposition assays. The MLE mutants with low-affinity TIRs had relatively lower transposition frequency from that of wild types. We conclude that TIR affinity to DBD significantly affects the transposition activity of Ppmar2. The mutant MLEs highly active TIRs constructed in this study can be used as a tool for bamboo genetic studies

Affinities of Terminal Inverted Repeats to DNA Binding Domain of Transposase Affect the Transposition Activity of Bamboo Ppmar2 Mariner-Like Element

Mariner-like elements (MLE) are a super-family of DNA transposons widespread in animal and plant genomes. Based on their transposition characteristics, such as random insertions and high-frequency heterogeneous transpositions, several MLEs have been developed to be used as tools in gene tagging and gene therapy. Two active MLEs, Ppmar1 and Ppmar2, have previously been identified in moso bamboo (Phyllostachys edulis). Both of these have a preferential insertion affinity to AT-rich region and their insertion sites are close to random in the host genome. In Ppmar2 element, we studied the affinities of terminal inverted repeats (TIRs) to DNA binding domain (DBD) and their influence on the transposition activity. We could identify two putative boxes in the TIRs which play a significant role in defining the TIR’s affinities to the DBD. Seven mutated TIRs were constructed, differing in affinities based on similarities with those of other plant MLEs. Gel mobility shift assays showed that the TIR mutants with mutation sites G669A-C671A had significantly higher affinities than the mutants with mutation sites C657T-A660T. The high-affinity TIRs indicated that their transposition frequency was 1.5–2.0 times higher than that of the wild type TIRs in yeast transposition assays. The MLE mutants with low-affinity TIRs had relatively lower transposition frequency from that of wild types. We conclude that TIR affinity to DBD significantly affects the transposition activity of Ppmar2. The mutant MLEs highly active TIRs constructed in this study can be used as a tool for bamboo genetic studies