Microbial Community Structure and Function in Peat Soil

Mnoga su tresetišta u Europi izlagana melioraciji i odvodnji, što je dovelo do promjena u procesima kruženja hranjivih tvari u tlu. Ovaj je rad sažetak objavljenih studija o mikrobnim procesima vezanim uz transformaciju ugljika i dušika u tlu Ljubljanskog barja. To je drenirano tresetište, smješteno nedaleko od Ljubljane, glavnoga grada Slovenije, poznato po bogatstvu biljnog i životinjskog svijeta. U radu je po prvi put dan širi pregled raznolikosti zajednice bakterija i arheja u tom organskoj tvari bogatom tlu, koje je izvor stakleničkih plinova, dušikovog oksida i ugljikovog dioksida, te ponor metana. U Ljubljanskom je barju metanogeneza ograničena velikim udjelom željeza, koje konkurira ostalim akceptorima elektrona. Osim toga, tlo je bogato vrlo aktivnim metanotrofima, naročito u slojevima tla s promjenjivom razinom podzemne vode. Denitrifikacija je ograničena akceptorima elektrona, a u dubljim slojevima tla i manjkom ugljičnih supstrata dostupnih za mikrobiološku razgradnju. Nitrifikacija je tla posljedica aktivnosti bakterija i arheja koje oksidiraju amonijak, pa je stupanj oksidacije amonijaka u Ljubljanskom barju među najvišim u svijetu. Zanimljivo, arheje iz odjeljka Thaumarchaeota u kiselim tresetištima uspijevaju samo na amonijaku što potječe iz organskog izvora i ne mogu oksidirati amonijak iz mineralnog izvora. U tlima je Ljubljanskoga barja pronađeno veliko bogatstvo gena što kodiraju bakterijske oksidoreduktaze slične lakazama. Uloga je tih enzima uglavnom nepoznata, a prema spoznajama o lakazama iz gljiva može se zaključiti da bakterijski enzimi sudjeluju u degradaciji lignina, oksidaciji različitih aromatskih i fenolnih spojeva, te oksidaciji metala. Budući su izazovi u ovom području istražiti specifične fiziološke uloge fenolnih oksidaza i ostalih enzima što sudjeluju u transformaciji tresetišta. Naše je poznavanje različitosti mikroorganizama u tresetištima, njihove funkcije i utjecaja na ekosustav još uvijek ograničeno, iako neophodno za učinkovito održavanje tresetišta, tih izvanrednih, ekološki značajnih, no osjetljivih staništa.Many peatlands in Europe have been subjected to land reclamation and systematic drainage, which have substantially affected nutrient cycles in the soil. This work reviews published studies on microbial processes linked to carbon and nitrogen transformations in the soils of the Ljubljana marsh, a drained peatland positioned close to Ljubljana, the capital of Slovenia. This region is known for its dramatic diversity of animal and plant life, but below ground it hides diverse bacterial and archaeal communities that are highly responsive to environmental changes and make the Ljubljana marsh soils a good source of N2O and CO2, and a sink for CH4. Methanogenesis is highly restricted in these soils due to competition for electron donors with iron reducers. In addition, methane is efficiently removed by methanotrophs, which are highly active, especially in the soil layers exposed to the changing water table. Denitrification is limited by electron acceptors and in deeper soil layers also by carbon, which becomes more recalcitrant with depth. Nitrification involves bacterial and archaeal ammonia oxidisers with ammonia oxidation rates being among the highest in the world. Interestingly, ammonia-oxidising Thaumarchaeota in acidic bog soils thrive only on ammonia released through mineralisation of organic matter and are incapable of oxidising added mineral ammonia. The soils of the Ljubljana marsh are rich in bacterial laccase-like genes, which may encode enzymes involved in lignin degradation and are therefore interesting for bioexploitations. Future challenges involve designing studies that will reveal specific physiological functions of phenol oxidases and other enzymes involved in peat transformations and address relations between microbial diversity, function and ecosystem responses to anthropogenic disturbances

The consequences of niche and physiological differentiation of archaeal and bacterial ammonia oxidisers for nitrous oxide emissions

The authors are members of the Nitrous Oxide Research Alliance (NORA), a Marie Skłodowska-Curie ITN and research project under the EU's seventh framework program (FP7). GN is funded by the AXA Research Fund and CGR by a Royal Society University Research Fellowship (UF150571) and a Natural Environment Research Council (NERC) Standard Grant (NE/K016342/1). The authors would like to thank Dr Robin Walker and the SRUC Craibstone Estate (Aberdeen) for access to the agricultural plots, Dr Alex Douglas for statistical advice and Philipp Schleusner for assisting microcosm construction and sampling.Peer reviewedPublisher PD

Thaumarchaeal Ammonia Oxidation in an Acidic Forest Peat Soil Is Not Influenced by Ammonium Amendment▿ †

Both bacteria and thaumarchaea contribute to ammonia oxidation, the first step in nitrification. The abundance of putative ammonia oxidizers is estimated by quantification of the functional gene amoA, which encodes ammonia monooxygenase subunit A. In soil, thaumarchaeal amoA genes often outnumber the equivalent bacterial genes. Ecophysiological studies indicate that thaumarchaeal ammonia oxidizers may have a selective advantage at low ammonia concentrations, with potential adaptation to soils in which mineralization is the major source of ammonia. To test this hypothesis, thaumarchaeal and bacterial ammonia oxidizers were investigated during nitrification in microcosms containing an organic, acidic forest peat soil (pH 4.1) with a low ammonium concentration but high potential for ammonia release during mineralization. Net nitrification rates were high but were not influenced by addition of ammonium. Bacterial amoA genes could not be detected, presumably because of low abundance of bacterial ammonia oxidizers. Phylogenetic analysis of thaumarchaeal 16S rRNA gene sequences indicated that dominant populations belonged to group 1.1c, 1.3, and “deep peat” lineages, while known amo-containing lineages (groups 1.1a and 1.1b) comprised only a small proportion of the total community. Growth of thaumarchaeal ammonia oxidizers was indicated by increased abundance of amoA genes during nitrification but was unaffected by addition of ammonium. Similarly, denaturing gradient gel electrophoresis analysis of amoA gene transcripts demonstrated small temporal changes in thaumarchaeal ammonia oxidizer communities but no effect of ammonium amendment. Thaumarchaea therefore appeared to dominate ammonia oxidation in this soil and oxidized ammonia arising from mineralization of organic matter rather than added inorganic nitrogen