HUR KAN VI VÅRDA MARKENS MIKROBER? Kristina Lindström

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1 HUR KAN VI VÅRDA MARKENS MIKROBER? Kristina Lindström Vårda markens mikrober Kristina Lindström

2 Vårda markens mikrober Kristina Lindström

3 FÖRHÅLLANDET MELLAN MARKENS HÄLSA OCH VÅR DH Wall et al. Nature 1-8 (2015) doi: /nature15744

4 DET SOM ÄR BRA FÖR MARKEN ÄR BRA FÖR OSS MARKENS BIODIVERSITET Artrikedom Funktionell diversitet Näringsvävarnas struktur Biotisk växelverkan Förluster leder till sämre ekosystemtjänster, flera patogener, mindre mat och rent vatten

5 FÖRHÅLLANDET MELLAN BIODIVERSITETEN, MARKANVÄNDNINGEN, MARKHÄLSAN OCH VÅR HÄLSA DH Wall et al. Nature 1-8 (2015) doi: /nature15744

6 ETT URVAL ORGANISMER UR MARKENS NÄRINGSVÄV RD Bardgett1 & WH van der Putten Nature 515, (2014) doi: /nature13855

7 ences in root morphology, as well as in the amount and type of rhizodeposits, between plants contribute greatly to this species-specific effect Specific metabolites released into the rhizosphere can trigger multiple responses in different soil microorganisms. For example, plant flavonoids can attract not only symbionts, such as Bradyrhizobium japonicum, but also pathogens, such the soil type, 4 9% of the operational taxonomic units detected by PhyloChip analysis were dependent on the cultivar 61. Crop-breeding programmes are typically con- MIKROBER I RHIZOSFÄREN ducted in monocropping systems under fertile conditions and in the absence of soil-borne pathogens, thus minimizing the contribution of the rhizosphere microbiome to plant growth and health. In this context, it has Rhizoplane Root hair AMF mykorrhiza Rhizosphere Bacterial nodule Mucilage Root cap rotknöl svamptrådar been. Root border cells Figure 2 The rhizosphere. The rhizosphere is a narrow zone of soil (a few millimetres wide) that surrounds and is influenced by plant roots. The schematic shows magnified pictures of the rhizosphere, containing saprophytic and symbiotic bacteria and fungi, including arbuscular mycorrhizal fungi (AMF). AMF inset modified, with permission, from REF. 158 (2008) Macmillan Publishers Ltd. All rights reserved. PGPR: Bakerier som inverkar på växten Vårda markens mikrober Kristina Lindström

8 SAMARBETE MELLAN OLIKA VÄXTER FACILITERING DELNING KOMPLEMETERING KVÄVE FOSFOR SPÅRÄMNEN MYKORRHIZA BLADVERKET ROTENS ARKITEKTUR GER ÖKAD EFFEKTIVITET Vårda markens mikrober Kristina Lindström

9 VAD GÖR MIKROBERNA I MARKEN? Äter: kol-, kväve-, fosforföreningar mm. Andas med eller utan syre Smälter maten: enzymer Växer Vilar,väntar Konkurrerar HUR VET VI ATT DE MÅR BRA? Mångsidig näring Lagom fukt Lagom syre Bakterier och svampar har skilda nischer Vårda markens mikrober Kristina Lindström

10 FÖR ATT BEDÖMA HUR DE MÅR MÄTER VI OLIKA PARAMETRAR KEMISK OCH FYSIKALISK BEDÖMNING AV DERAS MILJÖ Visuell bedömning Strukturen Vattenhållningskapacitet Mullhalten ph Halten av näringsämnen (kol, kväve, fosfor, kalium, övriga) Elektrisk ledningsförmåga MÄTNING AV DERAS AKTIVITET, MÄNGD OCH IDENTITET Markandning (koldioxid) Kvävetransformationer (nitrat, ammonium, lustgas) Biomassa Genetisk identitet (bakterier, svampar) Enzymatiska reaktioner Innehåll av olika funktionella gener Vårda markens mikrober Kristina Lindström

11 BAKTERIEISOLAT PÅ SKÅLAR GENOMGÅR ENZYMTEST Vårda markens mikrober Kristina Lindström

12 KVÄVETS KRETSLOPP BAKTERIERS LIVSVERK KVÄVEFIXERING NITRIFIKATION MINERALISERING DENITRIFIKATION KRETSLOPPET DRIVS HELT AV BAKTERIER

13 KVÄVEBUDGETEN VID VÄXTODLING An illustration of the N budget in crop production and resulting N species released to the environment. GASFORMIGA N-FÖRLUSTER N-TILLFÖRSEL MARKENS N-BORTFÖRSEL MED SKÖRDEN KVÄVE URLAKNINGS- OCH EROSIONSFÖRLUSTER X Zhang et al. Nature 1-9 (2015) doi: /nature15743

14 KVÄVEFIXERING I DET FINLÄNDSKA JORDBRUKET: BALJVÄXTER klöverarter, lucern, ärt, bondböna, lupin - Ympning av utsäde - Optimering av odlingsteknik (samodling,växelbruk) - Minimering av utsläpp (växthusgaser) Kristina Lindström

15 A RHIZOBIERNA HAR TVÅ LIV: BALJVÄXTERNAS KVÄVEFIXERING ÄGER RUM I RHIZOBIUM- BAKTERIER I ROTKNÖLARNA ENERGIN KOMMER FRÅN SOLEN NITROGENAS RHIZOBIER I MARKEN GER UPPHOV TILL ROTKNÖLAR OCH TRÄNGER IN I VÄXTEN Kristina Lindström: De fantastiska rhizobierna 15

16 BALJVÄXT (Galega) GRÄS (Bromus) UTSLÄPP AV LUSTGAS, N 2 O BART TRÄDA BALJVÄXT + GRÄS Kristina Lindström: 16

17 N2O-N total emission (g/ha) , , ,00 TRÄDA 1643,12 UTAN VÄXTTÄCKE STORA UTSLÄPP 1000,00 500,00 BROMUS 183,25 GALEGA 492,89 BROMUS + GALEGA 180,63 BROMUS + N 271,53 0,00 Bromus Fallow Galega Mixture Bromus+N Kristina Lindström and Miiro Jääskeläinen 17

18 N2O-UTSLÄPP UNDER VÄXTSÄSONGEN 2012 N- GÖDSEL TILLFÖRT SKÖRD Kristina Lindström: and Miiro Jääskeläinen 18

19 HUR IDENTIFIERAS MARKENS MIKROBER? - MED HJÄLP AV DERAS GENER JORDPROVER PROVTAGNING: Flera underprov från varje försöksruta kombineras 1g- för extraktion DNA- EXTRAKTION PCR SEKVEN- SERING DATABAS FÖR IDENTIFIERING ANALYS Vårda markens mikrober Kristina Lindström

20 MIKROBIELL DIVERSITET I EN VALL- JORD Sphingomonadaceae 2.09% uncultured 2.07% Nocardioidaceae 1.99% Chthoniobacteraceae 1.62% Roseiflexaceae 1.6% Solibacteraceae_(Subgroup_3) 3.7% WD2101_soil_group 3.33% KD4 96_fa 2.2% Bacteria_unclassified 3.85% Chitinophagaceae 5.81% Xanthobacteraceae 6.05% arter (OTU) klassificerade i 355 familjer BASERAR SIG PÅ ANALYS AV SPECIFIKA GENER Gemmatimonadaceae 9.66% Subgroup_6_fa 1.56% Alphaproteobacter ia_unclassified 1.41% Gaiellales_unclassified 1.3% Micromonosporaceae 1.3% Solirubrobacteraceae 1.24% Flavobacteriaceae 1.15% IMCC26256_fa 1.15% Blastocatellaceae 1.13% Cytophagales_unclassified Gammaproteobacter MB A2 108_fa Saccharimonadales_unclassified Subgroup_2_fa Bacillaceae Bdellovibrionaceae Polyangiaceae env.ops_17 Archangiaceae Fimbriimonadaceae Gaiellaceae Oxyphotobacter Parcubacteria_unclassified Kineosporiaceae Nocardiaceae RBG _fa Steroidobacteraceae Acidobacteriaceae_(Subgroup_1) Koribacteraceae Pseudomonadaceae Rhodanobacteraceae Sandaracinaceae bacteriap25 A4b BIrii41 CCD24_fa Chthonomonadales_f Deltaproteobacter Iamiaceae Paenibacillaceae Phycisphaeraceae Proteobacteria_unclassified 11 24_fa Anaerolineae_unclassified Armatimonadales_unclassified C0119_fa Cellulomonadaceae Chitinophagales_unclassified Fibrobacteraceae KD3 93 Lachnospiraceae OM190_fa Patescibacteria_unclassified Planctomycetes_unclassified Ruminococcaceae Subgroup_17_fa Verrucomicrobiaceae Xanthomonadales_unclassified A0839 AKYH767 Anaerolineaceae Chloroflexales_unclassified Clostridiales_unclassified FBP_fa Geminicoccaceae Geobacteraceae Hyphomonadaceae Methylophilaceae Micrococcales_unclassified Peptostreptococcaceae Planococcaceae Rhodobacteraceae Rhodocyclaceae Rubritaleaceae Spirosomaceae Streptosporangiaceae Subgroup_6_unclassified Weeksellaceae uncultured_fa G20 Alicyclobacillaceae Armatimonadaceae Armatimonadetes_unclassified BRC1_fa Bacillales_unclassified Bacteroidetes_unclassified Blfdi19 Cellvibrionaceae Chthoniobacterales_unclassified Corynebacteriales_unclassified Crocinitomicaceae Cyclobacteriaceae Diplorickettsiaceae Enterobacteriaceae Firmicutes_unclassified Gemmatimonadetes_unclassified Labraceae Legionellaceae NS11 12_marine_group NS9_marine_group Nannocystaceae Nostocaceae Paracaedibacteraceae Parachlamydiaceae Parcubacteria_fa Pla4_lineage_fa Prolixibacteraceae Rubinisphaeraceae SJA 28_fa Subgroup_22_fa Thermomonosporaceae Vermiphilaceae mle1 27 A21b ABY1_unclassified AT s2 59_fa Acetobacterales_unclassified Acidaminococcaceae Actinomycetaceae Aerococcaceae Aeromonadaceae Alteromonadaceae Amoebophilaceae Anaplasmataceae Arcobacteraceae Armatimonadales_fa Azospirillaceae BD2 11_terrestrial_group_fa Babeliales_fa Babeliales_unclassified Bacilli_unclassified Bacteriovoracaceae Bacteroidaceae Bacteroidales_unclassified Bacteroidetes_vadinHA17 Bifidobacteriaceae Blastocatellia_(Subgroup_4)_unclassified CHAB XI 27_fa CPR2_fa Candidatus_Adlerbacter Candidatus_Campbellbacter Candidatus_Kaiserbacter Candidatus_Komeilibacteria_fa Candidatus_Moranbacteria_fa Candidatus_Nomurabacteria_fa Candidatus_Pacebacteria_fa Candidatus_Peregrinibacteria_fa Candidatus_Peribacteria_fa Candidatus_Uhrbacter Candidatus_Vogelbacteria_fa Candidatus_Woesebacteria_fa Carnobacteriaceae Caulobacterales_unclassified Chitinibacteraceae Chlamydiales_unclassified Chloroflexaceae Christensenellaceae Chromobacteriaceae Clostridia_fa Clostridia_unclassified Clostridiaceae_2 Clostridiaceae_3 Clostridiaceae_4 Coleofasciculaceae Coriobacteriales_unclassified Corynebacteriaceae Coxiellaceae Cryptosporangiaceae Cyanobacteria_unclassified Dehalococcoidia_unclassified Deinococcaceae Demequinaceae Dermabacteraceae Desulfarculaceae Desulfobulbaceae Desulfuromonadaceae Desulfuromonadales_unclassified Dietziaceae Dysgonomonadaceae Eggerthellaceae Elusimicrobia_unclassified Endomicrobiaceae Enterococcaceae Erysipelotrichaceae Eubacteriaceae Family_III Family_XIII Family_XVIII Flavobacteriales_unclassified Frankiaceae Gallionellaceae Gastranaerophilales_fa Gracilibacteria_fa Gracilibacteria_unclassified Halieaceae Heliobacteriaceae Holosporaceae Hydrogenedensaceae Hymenobacteraceae Ignavibacteria_unclassified Inquilinaceae KD1 131 KI89A_clade_fa Kiloniellaceae Lactobacillales_unclassified Lentimicrobiaceae Leptospiraceae Lineage_IV_fa Magnetospirillaceae Methylomonaceae Methylophagaceae Micavibrionaceae Micavibrionales_unclassified Microgenomatia_unclassified Microtrichaceae Mollicutes_unclassified Moraxellaceae Muribaculaceae Myxococcaceae NB1 j_fa Nocardiopsaceae Nostocales_unclassified OPB56_fa Obscuribacterales_fa Oceanospirillales_unclassified Oligoflexaceae Omnitrophicaeota_fa P3OB 42 Paludibacteraceae Pasteuriaceae PeM15_fa Peptococcaceae Phaselicystidaceae Phycisphaerae_unclassified Planctomycetales_unclassified Prevotellaceae Procabacteriaceae Promicromonosporaceae Propionibacter Pseudohongiellaceae Puniceicoccaceae RCP2 54_fa Rhodospirillales_unclassified Rickettsiaceae Rickettsiales_unclassified Rikenellaceae S0134_terrestrial_group_fa SBR1031_fa SBR1031_unclassified SJA 15_fa SM1A07_fa SM2D12 Saccharimonadaceae Schlesneriaceae Selenomonadales_unclassified Simkaniaceae Sneathiellaceae Solimonadaceae Spirochaetaceae Spongiibacteraceae Sporichthyaceae Sporolactobacillaceae Staphylococcaceae Streptococcaceae Streptosporangiales_unclassified Subgroup_25_fa Sulfurospirillaceae Synergistaceae Syntrophomonadaceae Tannerellaceae Terrimicrobiaceae Thermoactinomycetaceae Thermodesulfovibrionia_unclassified Trueperaceae UBA12409 Veillonellaceae Verrucomicrobiales_unclassified WCHB1 41_fa WD260_fa WS2_fa WS4_fa WS6_(Dojkabacter 0% 0% 0.02% 0% 0.02% 0% 0.02% 0.02% 0.02% 0.02% 0% ia)_fa 0% 0.02% 0.02% 0.02% 0.04% ia_fa 0% 0% 0.02% 0.02% 0.02% ia_fa 0% 0% ia_fa 0% 0% 0% 0% 0% 0% 0.04% 0.02% 0.02% 0.02% 0.02% 0.02% 0.04% 0.04% 0.04% 0.04% 0.04% 0.04% 0.04% 0.04% 0.02% 0.02% 0.02% 0.04% 0.04% 0.04% 0.04% 0.06% 0.06% 0.06% 0.06% 0.06% 0.06% 0.06% 0.06% 0.06% 0.06% 0.06% 0.06% 0.06% 0.09% 0.09% 0.09% 0.09% ia_unclassified 0.09% 0.09% 0.06% 0.09% 0.06% a 0.09% 0.09% 0.11% 0.11% 0.11% 0.11% 0.11% 0.13% 0.13% 0.13% 0.11% 0.13% 0.15% ia_unclassified 0.15% 0.15% 0.17% 0.15% 0.15% 0.17% 0.17% 0.17% 0.19% 0.19% 0.19% ia_unclassified 0.21% 0.21% Acidobacteria_unclassified Clostridiaceae_1 0.21% 0.21% Mycobacteriaceae 1.13% TRA % Rhizobiales_Incer tae_sedis 0.26% Saprospiraceae Acidothermaceae 0.28% 0.26% Nitrosomonadaceae 1.13% Xanthomonadaceae 0.3% Subgroup_7_fa 0.3% Reyranellaceae 0.3% Microbacteriaceae 0.3% Acidimicrobiia_unclassified 1.09% Verrucomicrobiae_unclassified 0.32% Isosphaeraceae 0.32% Bacteroidia_unclassified 0.32% Acidobacteriales_unclassified 1.05% Caldilineaceae 0.32% Pirellulaceae 0.34% Devosiaceae 0.34% Burkholderiaceae 1.03% Unknown_Family 0.36% Sphingobacteriales_unclassified 0.36% Sphingobacter iaceae 0.36% Betaproteobacter iales_unclassified 1% Thermoleophilia_unclassified Caulobacteraceae 0.36% 0.38% Frankiales_unclassified 0.38% Gemmataceae 0.96% TK10_fa 0.43% Geodermatophilaceae 0.43% Myxococcales_unclassified 0.96% S085_fa 0.45% Saccharimonadales_fa 0.96% Micropepsaceae Nakamurellaceae 0.47% 0.47% Streptomycetaceae 0.47% Micrococcaceae 0.94% Pyrinomonadaceae 0.9% Pedosphaeraceae 0.85% Chloroflexi_unclassified 0.83% Microtrichales_unclassified Actinobacteria_unclassified 0.83% Methyloligellaceae Intrasporangiaceae 0.81% Microscillaceae 0.79% 0.75% 0.75% SC I 84 Hyphomicrobiaceae Rhizobiaceae 0.73% Acetobacteraceae Ilumatobacteraceae Nitrospiraceae Rhizobiales_unclassified Haliangiaceae Beijerinckiaceae Planctomycetacia_unclassified Subgroup_5_fa Pseudonocardiaceae 0.49% 0.47% 0.58% 0.49% 0.49% 0.6% 0.6% 0.68% 0.68% 0.64% 0.64% Vårda markens mikrober Kristina Lindström

21 BAKTERIERNA SAMVERKAR I NÄTVERK Vårda markens mikrober Kristina Lindström

22 BIOREMEDIERING AV OLJEFÖRORENAD JORD PROVTAGNING IDÉ: OLJEÄTANDE BAKTERIER I MARKEN UTNYTTJAS Förändringar i bakteriernas biomassa och diversitet i förhållande till oljekoncentration, miljöparametrar, skörd och provtagningstidpunkt 20/03/

23 BIOREMEDIERING EFFEKT AV OLJAN PÅ SPECIFIKA MIKROBER OCH DERAS DIVERSITET Olika arter reagerar olika Environmental Scienceand Pollution Research RESEARCH ARTICLE Bacterial community changes in response to oil contamination and perennial crop cultivation Aquabacterium Lysinimonas OTU 29 Microbacteriaceae Pseudorhabdys Lijuan Yan 1,2 &Petri Penttinen 1,3 &Anu Mikkonen 4 &Kristina Lindström 1 Received: 11 September 2017 /Accepted: 28February 2018 # Springer-Verlag GmbHGermany, part of Springer Nature2018 PROVTAGNINGSTIDPUNKTEN VIKTIG Abstract We investigated bacterial community dynamics in response to used motor oil contamination and perennial crop cultivation by 16S rrna gene amplicon sequencing in a 4-year field study. Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadeteswerethemajor bacterial phyla, and Rhodococcuswasthemost abundant genus. Initially, oil contamination decreased the overall bacterial diversity. Actinobacteria, Betaproteobacteria, and Gammaproteobacteria were sensitive to oil contamination, exhibiting clear Oljans succession with inverkan time. However, bacterial communities Grödans changed over inverkan time, regardless of oil contamination and crop cultivation. Theabundancedifference of most OTUs between oil-contaminated and non-contaminated plots remained the same in later sampling years after the initial abundance differenceinduced by oil spike. The abundances of three oil-favored actinobacteria (Lysinimonas, Microbacteriaceae, and Marmoricola) and one betaproteobacterium (Aquabacterium) changed in different manner over time in oil-contaminated and non-contaminated soil. We propose that these taxa are potential bio-indicators for monitoring recovery from motor oil contamination in boreal soil. The effect of crop cultivation on bacterial communities became significant only after the crops achieved stable growth, likely associated with plant material decomposition by Bacteroidetes, Armatimonadetes and Fibrobacteres. Keywords Soil microbiome. Hydrocarbon contamination. Bioremediation. Perennial crop cultivation. 16S rrna gene ampliconsequencing. Temporal abundancechange Responsible editor: Philippe Garrigues Electronicsupplementary material Theonlineversion of thisarticle ( supplementary material, which isavailableto authorized users. * Petri Penttinen petri.penttinen@helsinki.fi 1 Department of Environmental Sciences, University of Helsinki, PO Box 65, FI Helsinki, Finland Introduction Present address: Department of Environmental Sciences, University of Helsinki, Niemenkatu 73, FI Lahti,Finland Soil pollution by petroleum hydrocarbons (PHCs) originating from crude oil or refined petroleum productsposes a significant threat to the environment. In particular, used motor oil that contains high concentrations of aliphatics, polycyclic aromatic hydrocarbons (PAHs), and heavy metals (e.g., lead, zinc, chromium, barium, and arsenic) contributes to chronic hazards including carcinogenicity (Dominguez-Rosado et al. 2004; Vazquez-Duhalt 1989). Microorganisms can degrade PHCs and utilize them as carbon and energy sources in a natural attenuation pro- cess. Nitrogen is frequently a limiting factor 20/03/2019 in oil contaminated soils (Wenzel 2009). Thus, the nitrogen-

24 ODLINGSMARKEN KAN FÅNGA KOL Lal, R. Digging deeper: A holistic perspective of factors affecting soil organic carbon sequestration in agroecosystems Global Change Biology, Volume: 24, Issue: 8, Pages: , First published: 17 January 2018, DOI: ( /gcb.14054)

25 TILLSATSER I MARKEN muutaman vuoden välein, jolloin hyödyt kumuloivat. Maanparannuskuitujen levittämistä juuri ennen satokasvin kylvöä on hyvä välttää, sillä kuidut kuluttavat hajotessaan hetkellisesti maasta BIOKOL runsaasti happea ja typpeä. GIPS STRUKTURKALK OM N P S Ca Ravinnekuitu, Kotka, Luomu Ravinnekuitu, Imatra, Luomu Nollakuitu, Imatra, Luomu FIBRER Suositellun levitysmäärän sisältämät ravinteet. Soilfood Vårda markens mikrober Kristina Lindström

26 MARKHÄLSAN MARKENS VATTENKAPACITET MÄNSKLIGA DIMENSIONER MARKENS FUNTIONA LITET ENDOGENA FAKTORER I MARKEN EXOGENA FAKTORER R. Lal: Soil health and carbon management. Food and Energy Security 2016; 5(4): Vårda markens mikrober Kristina Lindström

27 Vårda markens mikrober Kristina Lindström