Добірка наукової літератури з теми "Microbial decomposers"

ABSTRACTCarrion decomposition is an ecologically important natural phenomenon influenced by a complex set of factors, including temperature, moisture, and the activity of microorganisms, invertebrates, and scavengers. The role of soil microbes as decomposers in this process is essential but not well understood and represents a knowledge gap in carrion ecology. To better define the role and sources of microbes in carrion decomposition, lab-reared mice were decomposed on either (i) soil with an intact microbial community or (ii) soil that was sterilized. We characterized the microbial community (16S rRNA gene for bacteria and archaea, and the 18S rRNA gene for fungi and microbial eukaryotes) for three body sites along with the underlying soil (i.e., gravesoils) at time intervals coinciding with visible changes in carrion morphology. Our results indicate that mice placed on soil with intact microbial communities reach advanced stages of decomposition 2 to 3 times faster than those placed on sterile soil. Microbial communities associated with skin and gravesoils of carrion in stages of active and advanced decay were significantly different between soil types (sterile versus untreated), suggesting that substrates on which carrion decompose may partially determine the microbial decomposer community. However, the source of the decomposer community (soil- versus carcass-associated microbes) was not clear in our data set, suggesting that greater sequencing depth needs to be employed to identify the origin of the decomposer communities in carrion decomposition. Overall, our data show that soil microbial communities have a significant impact on the rate at which carrion decomposes and have important implications for understanding carrion ecology.

We studied the short-term responses of decomposers to different forest harvesting methods in a boreal spruce forest (Picea abies (L.) Karst.). We hypothesised that the less intensive the forest harvesting method is, the fewer changes occur in the decomposer community. The treatments, in addition to untreated controls, were (1) selection felling (30% of the stand volume removed), (2) retention felling (tree patches retained), (3) clear felling, (4) gap felling without and (5) with harrowing. Microbial community structure (phospholipid fatty acids (PLFA) pattern) changed in the first year, microbial biomass and basal respiration decreased in the second year, and density of the enchytraeid worm Cognettia sphagnetorum (Vejd.) increased in the third year after the clear felling. The community of collembolans did not respond to forest harvestings. Although there were changes in the microbial community, the invertebrates at higher trophic levels did not parallelly respond to these changes. The selection felling had no influence on the decomposers, while the gap fellings induced an increase in the numbers of enchytraeids in harvested gaps. We conclude that the decomposers of the coniferous forest soils are well buffered against initial environmental changes resulting from forest harvesting, and also that the PLFA pattern is a sensitive indicator of changes in the microbial community induced by forest harvesting.

The objective of this study was to investigate the possibility of using microbial strains as residue decomposers and to determine the effect of these strains on chemical and microbial properties in the residue-amended soil. Greenhouse experiment consisted of eight Bacillus treatments, three Trichoderma treatments, and their combination, all applied to non-sterile chernozem soil amended with wheat straw. Incorporation of wheat straw improved soil chemical and microbial properties, while the extent of residue decom?position under microbial strains was intensified. Microbial treatments significantly affected the soil pH, the content of carbonate, total carbon, soil organic carbon, humus, and available phosphorus and potassium. Bacterial and fungal treatments also significantly influenced the total microbial number, ammonifiers, N2-fixers, fungi, actinomycetes, oligotrophs, copiotrophs, and cellulolytic microorganisms. The effect of microbial treatments varied depending on the applied strains and examined properties, with Bacillus strains being more promising residue decomposers compared to Trichoderma strains. The most effective microbial strains could be used as potential decomposers of crop residues.

Peatlands are a dominant landform in the northern hemisphere, accumulating carbon in the form of peat due to an imbalance between decomposition and plant production rates. Decomposer (saprobes) and mycorrhizal fungi significantly influence carbon dynamics by degrading organic matter via the synthesis of extracellular enzymes. As organic matter decomposes, litter quality variables figure most prominently in the succession of fungi. Hence, litters composed primarily of complex polymers decompose very slowly. Surprisingly, recalcitrant polymer degraders (mostly basidiomycetes) are rarely isolated from peat, which may explain the accumulation of complex polymers in peat profiles. While enzymatic profiles of mycorrhizal fungi and other root endophytes may be more limited compared with saprobes, many of these fungi can degrade polymers of varying complexity as well and hence may also be significant decomposers of organic matter. To date, anamorphic ascomycetes and zygomycetes are the most frequently isolated fungi from peatlands (63 and 10% of all taxa, respectively), and chytridiomycetes, teleomorphic ascomycetes, and basidiomycetes appear to be less common (11% of all taxa). The remaining 16% of taxa remain unidentified or are sterile taxa. How disturbances affect peatland microbial communities and their roles is virtually unknown. This aspect of peatland microbial ecology requires immediate attention. The objective of this paper is to review the current state of knowledge of the diversity of fungi and their roles in carbon cycling dynamics in peatlands. Key words: Peatlands, fungi, carbon dynamics, diversity, functions, saprobes, mycorrhizas

Phylogenetic distances of coexisting species differ greatly within plant communities, but their consequences for decomposers and decomposition remain unknown. We hypothesized that large phylogenetic distance of leaf litter mixtures increases differences of their litter traits, which may, in turn, result in increased resource complementarity or decreased resource concentration for decomposers and hence increased or decreased chemical transformation and reduction of litter. We conducted a litter mixture experiment including 12 common temperate tree species (evolutionarily separated by up to 106 Myr), and sampled after seven months, at which average mass loss was more than 50%. We found no effect of increased phylogenetic distance on litter mass loss or on abundance and diversity of invertebrate decomposers. However, phylogenetic distance decreased microbial biomass and increased carbon/nitrogen (C/N) ratios of litter mixtures. Consistently, four litter traits showed (marginally) significant phylogenetic signal and in three of these traits increasing trait difference decreased microbial biomass and increased C/N. We suggest that phylogenetic proximity of litter favours microbial decomposers and chemical transformation of litter owing to a resource concentration effect. This leads to a new hypothesis: closely related plant species occurring in the same niche should promote and profit from increased nutrient availability.

A field experiment was conducted at Jorhat, Assam during 2004-05 and 2005-06 to find out an effective prac- tice of rice (Oryza sativa L.) straw management in wheat (Triticum aestivum L. emend. Fiori & Paol.) as a compo- nent of integrated nutrient management. Straw was incorporated @ 5 tlha with different decomposers, viz. starter N (one-third recommended dose of N), cellulose-decomposing microorganisms (CDM), earthworms culture (EC), EC + FYM, CDM + EC, FYM and starter N+ CDM + EC + lime. These decomposers significantly improved the yield and yield components in wheat compared with straw removal. Incorporation of rice straw @ 5 Vha under dual in- oculation of cellulose-decomposing microorganisms and earthworms improved the grain yield by 2.46 Vha. These also increased the nutrient uptake, available N, P, K in soil at harvest and benefit : cost ratio. Straw incorporation increased the organic C in the soil by 2-1 1% compared with straw removal. It also increased the microbial popula- tion in soil substantially irrespective of the decomposer used. Inoculation with CDM led to build-up of microbial population in the soil. Thus, rice straw incorporation with cellulose decomposing micro-organisms and earthworms resulted in higher yield, increased nutrient uptake, improved residual soil fertility and soil microorganism status and ultimately higher benefit : cost ratio of wheat.

Microbial N2-fixer and P-solubilizer were innoculated in a mixture of fresh manure and phosphate rock formulated as an Organonitrophos fertilizer. The population dynamics of bacteria and fungi growing during the composting process were observed. The inoculation treatments consisted of: K = mixture of 20% phosphate rock and 80% of fresh manure + decomposers (control), N = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + N2-fixer (Azotobacter and Azospirillum sp.) , P = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + P-solubilizer (A. niger and P. fluorescens), and NP = mixture of 20% phosphate rock and 80% of fresh manure + decomposers + N2-fixer + P-solubilizer. The results showed that inoculation of microbial N2-fixer and combination inoculation of N2-fixer and P-solubilizer increased the total bacterial population compared to that of the control as well as the only inoculation of microbial P-solubilizer on the 14th day of observation in which the bacteria reached the highest population. On all the observation days, the population of fungi in the inoculation of microbial P-solubilizer treatment increased significantly compared to that of the control. However, there was no difference between the populations of fungi in the inoculation of N2-fixer and combination inoculation of N2-fixer and Psolubilizer. The genus of fungy identified in the compost of the mixture of fresh manure and phosphate rock were Chytridium sp., Aspergillus sp., Rhizopus sp., and Fusarium sp.[How to Cite : Nugroho SG, Dermiyati, J Lumbanraja, S Triyono, H Ismono. 2013. Inoculation Effect of N2-Fixer and P-Solubilizer into a Mixture of Fresh Manure and Phosphate Rock Formulated as Organonitrofos Fertilizer on Bacterial and Fungal Populations. J Trop Soils, 18 (1): 75-80. doi: 10.5400/jts.2013.18.1.75][Permalink/DOI: www.dx.doi.org/10.5400/jts.2013.18.1.75]

Leaf litter decomposition in lowland tropical forests represents a significant flux of carbon (C) to the atmosphere, and is controlled by both extrinsic site conditions and intrinsic litter traits. However, there is a gap in the understanding about the relative importance of these two factors, and of the role of interactions between them. Global change drivers, such as mean annual precipitation (MAP) change and soil nitrogen (N) fertilisation by deposition, could affect both pathways simultaneously. In order to predict the response of the global C cycle to future change, a further understanding of such interactions is required, and is the focus of this thesis. Using a range of experimental factorial studies, in the field and laboratory, in mature tropical forests in Panama, the relative and interactive effects on decomposition of MAP, soil N and phosphorus (P) availability, litter species identity, and litter N and P status, were determined. Leaf litter species identity was a significant predictor of decomposition across the landscape, whilst soil C:N ratio was more important than MAP. Within species, elevated P concentration and decreased N:P ratio in litter was associated with decreased C mineralisation. Increased soil N availability altered microbial community composition, which increased decomposition of some leaf litter types. The results highlight litter traits as an important driver of decomposition via species identify and intra-species leaf litter chemistry. Also, the implications of decomposer activity and composition for decomposition will depend on litter traits. This thesis contributes valuable research evidence to augment current understanding of the importance of litter traits, and their interactions with decomposers, as a pathway through which global change drivers could affect the C cycle in tropical forests.

La décomposition de la litière végétale est un processus fondamental de l'écosystème et la principale source d'énergie et de nutriments dans les cours d'eau. Toute altération de ce processus peut entraîner des conséquences importantes sur le cycle des nutriments. Les décomposeurs, y compris les hyphomycètes aquatiques (HA) et les bactéries hétérotrophes, jouent un rôle central dans la décomposition, mais leurs exigences stœchiométriques et leur plasticité élémentaire restent peu étudiées. Alors que les décomposeurs ont besoin de nutriments inorganiques pour équilibrer leurs besoins élémentaires lors de la décomposition de la litière végétale appauvrie en nutriments, les ratios élémentaires optimaux spécifiques pour les espèces et les communautés de décomposeurs restent largement inconnus. Les résultats d'études expérimentales menées en conditions contrôlées ont permis de confirmer la large plasticité élémentaire de la biomasse fongique, tant à l'échelle individuelle qu'à l'échelle de la communauté. Cette plasticité est apparue plus importante pour le phosphore (P) que pour l'azote (N), et l'immobilisation des nutriments s'est produite rapidement (observée pour le P inorganique après 18 h d'ajout de nutriments). En évaluant la décomposition de la litière de feuilles le long des gradients N:P, les communautés de décomposeurs comprenant les HA — mais pas les bactéries seules — ont pu maintenir des intensités élevées de décomposition même à des teneurs en P extrêmement faibles et lorsque N était suffisant, suggérant des capacités élevées des HA à remobiliser leur P interne. De plus, la quantification de l'abondance relative des espèces dans les assemblages de HA a suggéré que les traits stœchiométriques individuels participaient à la distribution des espèces le long du gradient N:P, mais qui n'étaient pas suffisants pour expliquer entièrement les structures des assemblages. Contrairement aux assomptions générales et bien qu'elle soit liée au gradient N:P disponible, la minéralisation des nutriments (c'est-à-dire la libération nette de nutriments inorganiques de la litière) est restée limitée, mais le processus d'immobilisation des nutriments était dominant, du moins pendant la durée de nos expériences. Enfin, les contaminants et la variation de température ont pu modifier de manière significative les ratios N:P optimaux pour la décomposition par les décomposeurs. Ces résultats suggèrent des impacts importants — et potentiellement prédictible — de ces stresseurs sur l'intensité et la dynamique de la décomposition microbienne de la litière végétale. Les résultats de ces travaux confirment que la combinaison de traits stœchiométriques avec d'autres traits écologiques et biologiques permettrait certainement de comprendre plus en profondeur le processus de décomposition et sa réponse aux changements globaux
Decomposition of plant litter is one of the most important processes driving ecosystem functioning, it is the main energy and nutrient source in forested headwater streams. Any impairment of this process can have significant consequences for nutrient cycling. Decomposers, including aquatic hyphomycetes (AH) and heterotrophic bacteria, play a central role in decomposition, but their stoichiometric requirements and elemental plasticity remain understudied. While decomposers require inorganic nutrients to balance their stoichiometric requirements when breaking down nutrient-depleted plant litter, the specific optimal elemental ratios for species and communities of decomposers remain largely unknown. Results of different experimental studies carried out in controlled conditions first allowed to confirm the wide elemental plasticity of fungal biomass, both at the individual and at the assemblage/community scales. This plasticity appeared greater for phosphorus (P) than for nitrogen (N), and nutrient immobilisation occurred very quickly (observed for inorganic P after an 18h of nutrients addition). When evaluating leaf litter decomposition along N:P gradients, decomposer communities containing AH - but not bacteria alone - were able to maintain the decomposition process at high levels even at extremely low P contents and when N was sufficient, suggesting high capacities of AH to remobilise their internal P. Also, quantification of species relative abundances in AH assemblages suggested that individual stoichiometric traits participated to species distribution along the N:P gradient but were not sufficient to entirely explain assemblage structures. Contrary to common assumptions, while related to available N:P gradient, nutrient mineralisation (i.e. net release of inorganic nutrients from plant litter) remained limited, and nutrient immobilisation was the dominant process, at least for the duration of our experiments. Finally, both contaminants and temperature variations were able to significantly change the optimal N:P ratios for litter decomposition by decomposer communities, suggesting large - and potentially predictable - impacts of these stressors on the intensity and the dynamic of microbial decomposition of plant litter in ecosystems. All the results from these studies confirm that combining stoichiometric traits with other ecological and biological traits would certainly allow our understanding in depth, the decomposition process, and its response to global changes

Microorganisms are known to be agents involved in the decomposition of organic matter. However, little is known about the participation of the microbial communities during the decomposition of mammalian skeletal muscle tissue. This study investigates the capacity of the soil microbial community to adapt to the decomposition of skeletal muscle tissue in differing soils. This has implications for the study of mass graves and sites of repeated burial. A controlled laboratory experiment was designed to assess the adaptability of microbial communities present in three distinct soil types (sand, loamy sand and sandy clay loam) found near Perth, Western Australia. This experiment was split into two main stages. The initial decomposition stage involved the addition of porcine skeletal muscle tissue (SMT) (Sus scrofa) to each of the three soil types which were then left to decompose for a period of time. Controls were run in parallel, which had no porcine SMT present. The second decomposition stage involved a second addition of SMT to the soils obtained from the initial decomposition stage. Therefore, for each soil, SMT was either decomposed in the soil that had been pre-exposed to SMT or not. The rate of decomposition, microbial activity (CO2 respiration) and microbial biomass (substrate-induced respiration) were monitored during the second decomposition stage. The functional diversity of the microbial populations in the soil were assessed using Community-Level Physiological Profiling (CLPP). Across the three soil types, the re-introduction of SMT to the soil has led to its enhanced decomposition (measured by tissue mass loss and microbial activity) by the microbial communities. This microbial adaptation may have been facilitated by a functional change in the soil microbial communities.

Tese de Doutoramento em Ciências
Human activities are threatening biodiversity in freshwaters leading to irreversible alterations in ecosystem processes. One of the most important processes for the functioning of small-forested streams is the decomposition of allochthonous plant litter, which constitutes the major source of nutrients and energy for freshwater food-webs. Microbial decomposers, namely fungi and bacteria, play a critical role in this process degrading leaf material and increasing leaf palatability for invertebrate shredders. An obvious question that arises is in what extent pollution can affect the diversity of microbial decomposers altering the functions they perform in freshwater ecosystems. In a microcosm experiment, we showed that the loss of aquatic fungal species affected fungal biomass and reproduction, but not leaf mass loss. Complementarity effects appeared to occur between fungal species because multicultures had higher performances than those expected from individual performances in monocultures. Moreover, lower fungal biomass and leaf mass loss were found in the absence of Articulospora tetracladia and species identity affected all measured parameters. In a transplant experiment, we investigated how a community of microbial decomposers adapted to a reference site responds to a sudden decrease in the water quality. The transfer of leaves colonized at a reference site to a site with high concentration of nutrients and heavy metals in the stream water reduced fungal diversity and sporulation, but not fungal biomass and leaf decomposition. This suggests that high diversity of fungi may mitigated the impact of anthropogenic stress in streams. Most studies addressing microbial diversity on decomposing leaves rely on the microscopic identification of fungal conidia and on the number of bacterial morphotypes. However, the production of conidia by fungi varies with the species and it is affected by several environmental factors. On the other hand, bacteria have few morphological differences, making it difficult to accurately assess microbial diversity. In our work, DNA fingerprinting techniques were successfully used for assessing fungal and bacterial diversity. Denaturing gradient gel electrophoresis (DGGE) showed a more diverse microbial community on decomposing leaves than microscopic techniques. Moreover, DGGE allowed detecting shifts in microbial communities during leaf decomposition and under different stress conditions (eutrophication and metal pollution). The structure of fungal and bacterial communities on decomposing leaves changed along a gradient of inorganic nitrogen and phosphorus in streams, as indicated by canonical correspondence analysis based on the morphology of fungal conidia and on DNA fingerprinting. Sporulation was depressed in the most eutrophic streams, while bacterial biomass appeared to be stimulated, except in the presence of high nitrites and ammonium concentrations. Leaf decomposition rate was stimulated at only one site with moderate eutrophication. The exposure of naturally colonized leaves to environmentally realistic concentrations of copper and zinc alone or in mixtures showed that metal exposure altered the structure of fungal and bacterial communities on decomposing leaves. Exposure to metal mixtures or to the highest Cu concentration significantly reduced leaf decomposition rates and fungal reproduction, but not fungal biomass. Bacterial biomass was strongly inhibited by all metal treatments. Moreover, the combined effects of Cu and Zn on microbial decomposition of leaf litter were mostly additive, because observed effects did not differ from those expected as the sum of single metal effects. However, antagonistic effects on bacterial biomass were found in all metal combinations and on fungal reproduction in metal combinations with the highest Cu concentrations, particularly at longer exposure times. Moreover, the sequence by which metals were added to microcosms affected fungal biomass and sporulation, but not bacterial biomass, probably because microbial sensitivities to the metals were different. The resistance of microbial decomposers to Cu did not increase when communities were previously acclimated to Zn and vice-versa. Microbial decomposers could be expending considerable energy to maintain their functions under the stress imposed by the first metal and if so, species resistance might be diminished when the second metal was added. After release from metals, the structure of fungal communities became similar to that of control, as indicated by the principal response curves of sporulating species and also by the DGGE analyses. A recovery of the microbial activity seemed also to occur, as shown by the lack of differences in leaf mass loss, bacterial biomass and fungal reproduction between control and metal treatments.
As actividades humanas estão a ameaçar a biodiversidade dos ecossistemas aquáticos, conduzindo a alterações irreversíveis no seu funcionamento. Um dos processos mais importantes para o funcionamento dos ecossistemas de rios de baixa ordem é a decomposição de detritos vegetais alóctones, que constituem a principal fonte de carbono e energia para as cadeias alimentares nesses sistemas de água doce. Os microrganismos decompositores aquáticos, nomeadamente os fungos e as bactérias, desempenham um papel fundamental na decomposição dos detritos vegetais e aumentam a sua palatabilidade para os invertebrados trituradores. Uma questão relevante no âmbito da Ecologia actual é a de saber se a poluição afecta a biodiversidade e quais os impactos para o funcionamento dos ecossistemas aquáticos. Numa experiência em microcosmos, mostrámos que a perda de espécies de fungos aquáticos afectava a biomassa e a reprodução dos fungos, mas não a decomposição de folhada. As espécies de fungos pareceram exibir efeitos de complementaridade uma vez que as culturas mistas tiveram desempenhos superiores ao esperado a partir dos desempenhos em cultura pura. Contudo, a identidade das espécies afectou todos os parâmetros analisados. Além disso, a biomassa dos fungos e a perda de massa foliar foram menores na ausência de Articulospora tetracladia. Numa experiência de transplante de folhas entre rios, investigámos como uma comunidade de microrganismos decompositores adaptados a um local de referência responde a um declínio abrupto na qualidade da água. A transferência de folhas colonizadas num local de referência para um local com concentrações elevadas de nutrientes e metais pesados na água reduziu a diversidade e a esporulação dos fungos, mas não a sua biomassa e a decomposição foliar. Isto sugere que uma elevada diversidade de fungos pode contribuir para atenuar o impacto de stressores antropogénicos nos rios. A maioria dos estudos efectuados tem analisado a diversidade de microrganismos associados a folhas em decomposição com base na identificação microscópica das conídias libertadas pelos fungos e nos tipos morfológicos de bactérias. No entanto, a produção de conídias pelos fungos varia com a espécie e é afectada por vários factores ambientais. Por outro lado, as bactérias possuem poucas diferenças morfológicas entre si, tornando difícil avaliar com exactidão a diversidade microbiana. No nosso trabalho, a electroforese em gradiente desnaturante (DGGE) do DNA microbiano mostrou uma comunidade de fungos e de bactérias mais diversa em folhas em decomposição do que as técnicas de microscopia. O DGGE permitiu detectar alterações na estrutura das comunidades durante a decomposição foliar e em diferentes condições de stresse (eutrofização e poluição por metais). A estrutura das comunidades de fungos e de bactérias nas folhas em decomposição sofreu alterações ao longo de um gradiente de azoto e de fósforo nos rios, como indicado pelas análises de correspondência canónica baseadas na morfologia das conídias dos fungos e no perfil de DGGE. A esporulação diminuiu nos rios mais eutrofizados, enquanto que a biomassa de bactérias pareceu ser estimulada, excepto na presença de concentrações elevadas de nitritos e amónia. A taxa de decomposição foliar foi estimulada apenas num dos locais com eutrofização moderada. A exposição de folhas colonizadas naturalmente a concentrações de cobre e de zinco, ambientalmente realísticas, alterou a estrutura das comunidades de fungos e de bactérias nas folhas em decomposição. A exposição às misturas de metais ou à concentração de Cu mais elevada reduziu significativamente a taxa de decomposição foliar e a reprodução dos fungos, mas não inibiu a biomassa dos fungos. A biomassa bacteriana foi inibida em todos os tratamentos com metais. Além disso, os efeitos combinados do Cu e do Zn na decomposição microbiana da folhada foram maioritariamente aditivos, uma vez que os efeitos observados não diferiram dos esperados a partir da soma dos efeitos de cada metal isolado. No entanto, foram observados efeitos antagonísticos na biomassa de bactérias, em todas as combinações de metais, e na reprodução de fungos nas combinações contendo Cu na concentração mais elevada, particularmente em tempos mais longos de exposição. A sequência pela qual os metais foram adicionados aos microcosmos afectou a biomassa e a esporulação dos fungos, mas não a biomassa das bactérias provavelmente porque a sensibilidade dos microrganismos aos dois metais era diferente. A resistência dos microrganismos decompositores ao Cu não aumentou quando as comunidades foram previamente aclimatadas ao Zn e vice-versa. Os microrganismos poderiam estar a consumir uma fracção de energia considerável para manter as suas funções na presença do primeiro metal e, por este motivo, a sua resistência poderia estar diminuída quando o segundo metal foi adicionado. Após libertação do stresse metálico, a estrutura das comunidades de fungos tornou-se semelhante à das comunidades controlo, como indicado pelas curvas de resposta principal das espécies identificadas a partir dos esporos e pela análise de DGGE. Além disso, a actividade microbiana pareceu recuperar após a libertação do stresse metálico, como sugerido pela ausência de diferenças na perda de massa foliar, na biomassa das bactérias e na reprodução dos fungos entre o controlo e os tratamentos com metais.
Fundação para a Ciência e a Tecnologia (FCT) - SFRH/BD/13482/2003.

Dissertação de Mestrado em Ecologia, apresentada ao Departamento de Ciências da Vida da Faculdade de Ciências e Tecnologia da Universidade de Coimbra.
A taxa de decomposição microbiana de folhas senescentes em rios e a riqueza em taxa de fungos e bactérias aquáticas foram estudados ao longo de um gradiente de altitude em dois sistemas, 1600-3800 m snm no Equador (ecossistema tropical a 0 ° Lat) e 1992-3200 m snm em Colorado EUA (ecossistema temperado a 40 ° N). Sacos de malha fina (0,5 mm) contendo folhas de amieiro nativo em cada una das zonas (Equador: Alnus acuminata Kunth; Colorado: Alnus incana (L.) Moench) foram incubadas em cinco locais ao longo do gradiente de altitude em cada latitude e recuperados em datas de amostragem selecionados para determinar as taxas de decomposição e a diversidade de decompositores. As taxas de decomposição (k) foram mais rápidos em Colorado (0,0197-0,0453 gama de valores) do que no Equador (0,0065 - 0.014). No Equador a decomposição diminuiu com a elevação (regressão linear, p <0,001; R2 = 0.95), o que foi explicado pela diferença de temperatura entre locais. Em Colorado a decomposição não mudo com a altitude (regressão linear, p = 0,48; R2 <0,001) e não esteve ligada a nenhum dos parâmetros ambientais registrados. Os nitratos no Colorado foram ~ 30 vezes mais elevada do que no Equador (11,28 vs 0,40 mg / L; t-test, p = 0.04) podendo o seu efeito sobrepor-se ao da temperatura. A diversidad de microrganismos decompositores foi estimada aplicando a eletroforese em gel com gradiente desnaturante (DGGE), avaliando o DNA ribossomal (rDNA) para fungos aquático (região ITS2) e bactérias (V3 região variável). A diversidade de fungos aquáticos no Equador aumentou com a elevação (regressão linear, p = 0.03; R2 = 0.83), enquanto no Colorado o número máximo de taxa atingiu um pico em altitudes médias (regressão polinomial; p = 0.7; R2 = 0.57). Os três primeiros eixos de uma “análise de componentes principais” (PCA) no Equador explicaram 93% da variabilidade total e o número de OTUs em fungos esteve relacionada com PO4, que foi maior nos locais mais altos e desceu para os locais mais baixos. No Colorado, os três eixos da PCA explicaram 92% da variabilidade total e a riqueza de taxa foi relacionada com CPOM, baixa profundidade da água e concentrações moderadas de NO3. O número de taxa para fungos registrados no Equador e no Colorado (13.3 e 15.2 OTUs) não foi estatisticamente diferente (teste t; p = 0.2; t = 1.43; df = 8). A análise MDS usando o coeficiente de similaridade de Bray-Curtis mostrou que a identidade dos OTUs em Colorado e Equador foi diferente. As unidades taxonómicas das bactérias no Equador e Colorado diminuiu com a altitude (regressão linear; p = 0,0001; R2 = 0.58 e p = 0.0004; R2 = 0.99, respetivamente). O maior número de OTUs ao longo do gradiente equatoriana foi correlacionado principalmente com o segundo eixo do PCA, que por sua vez se correlaciona com CPOM, NO3 e NO2. Em Colorado a variabilidade dos taxa foi negativamente correlacionada com o primeiro eixo do PCA, o qual foi correlacionado principalmente com concentrações de temperatura e NO3. A comunidade das bactérias exibiu uma distribuição cosmopolita, i.e., não houve diferenças na identidade entre Equador e Colorado (MDS; stress value: 0.19). A dissimilaridade entre as comunidades ao longo dos gradientes de altitude (β diversidade) foi menor no Equador do que em Colorado para fungos aquáticos (ANOSIM, p = 0.51; global R = 0.004 vs p = 0.003; global R = 0.54) e bactérias (ANOSIM, p = 0.54; R = -0.021 global vs. p = 0.003; global R = 0.51). Estes resultados sugerem que (1) A taxa de decomposição é um processo dependente da temperatura, mas que pode ser mascarada por outros fatores, tais como nutrientes na água. (2) A riqueza de espécies e a composição da comunidade de microrganismos decompositores pode ser controlada por variáveis ambientais locais, como os nutrientes dissolvidos na água e características de substrato (qualidade das folhas), o que sugere que os padrões observados em organismos de grandes dimensões pode não afetar aos organismos de menor tamanho. Além disso, a riqueza latitudinal de espécies pode ser dificilmente observada ao longo de um gradiente de altitude, caso a temperatura seja o principal fator ambiental que controla a diversidade e o turnover de espécies, uma vez que as alterações térmicas na água são menores do que for a dela.
The microbial decomposition rate and species richness of aquatic fungi and bacteria were studied along an altitudinal gradient from 1600 to 3800 m.a.s.l. in Ecuador (tropical ecosystem at 0° Lat) and from 1992 to 3200 m.a.s.l. in Colorado US (temperate ecosystem at 40°N). Fine mesh bags (0.5 mm) containing native alder leaves from tropical (Alnus acuminata Kunth) and temperate (Alnus incana (L.) Moench) zones were incubated in five locations along the altitudinal gradient at each latitude and retrieved at selected sampling dates to decomposition rates and diversity of decomposers. Decomposition rates (k) were faster in Colorado (0.0197 - 0.0453 range) than in Ecuador (0.0065 - 0.014 range). In Ecuador litter decomposition decreased with elevation (linear regression, p < 0.001; R2 = 0.95), which was explained by temperature difference across sites. In Colorado litter decomposition did not change with altitude (linear regression, p = 0.48; R2 < 0.001) and was not related to any of the measured environmental parameters. Nitrates in Colorado were ~30 fold higher than in Ecuador (11.28 vs. 0.40 μg/L; t-test, p = 0.04) and might be overridden the temperature effect. Microbial decomposers diversity was estimated applying the denaturing gradient gel electrophoresis (DGGE) technique and assessing the ribosomal DNA (rDNA) for aquatic fungi (ITS2 region) and bacteria (V3 variable region). Aquatic fungi diversity in Ecuador increased with elevation (linear regression, p = 0.03; R2 = 0.83), whereas in Colorado the maximum number of taxa peaked at middle altitudes (polynomial regression; p = 0.7; R2 = 0.57). The three PCA axis in Ecuador explained 93% of the total variability and the number of fungal OTUs related with PO4. In Colorado, the three PCA axis explained 92% of the total variability and taxa richness was related with CPOM standing stock, shallow waters and moderate concentrations of NO3. The number of fungal taxa recorded in Ecuador and Colorado (13.3 and 15.2 OTUs) was not statistically different (t-test; p = 0.2; t =1.43; df = 8). The MDS analysis using Bray-Curtis similarity coefficient determined that fungi taxa is biogeographically distributed by latitude. Bacteria taxa units in Ecuador and Colorado decreased with altitude (linear regression; p = 0.0001; R2 = 0.58 and p = 0.0004; R2 = 0.99). The higher number of OTUs along the Ecuadorian gradient was primarily correlated with the 2nd PCA axis, which in turn was correlated with CPOM standing stock, NO3 and NO2. In Colorado the taxa variability was negatively correlated with the first PCA axis, which was mainly correlated with temperature and NO3 concentrations. Bacteria community exhibited a cosmopolitan distribution (MDS; stress value: 0.19). The dissimilarity among communities along the altitudinal gradients (β diversity) was lower in Ecuador than in Colorado for aquatic fungi (ANOSIM, p = 0.51; Global R= 0.004 vs. p = 0.003; Global R= 0.54) and bacteria (ANOSIM, p = 0.54; Global R= -0.021 vs. p = 0.003; Global R= 0.51). These results suggest that (1) litter decomposition is a temperature dependent process, which can be overridden by other factors such as nutrients in the water. (2) Species richness and the community composition of microbial decomposers may be controlled by local environmental variables, such as dissolved nutrients in water and substrate characteristics (leaf quality), which may imply that broadly patterns observed on large organisms might not affect small size organisms. Besides, latitudinal species richness tendency might be barely observed along an altitudinal gradient, considering the temperature as the mainly environmental factor driving the diversity and the taxa turnover.

Microorganisms are the unseen majority that determines ecosystem processes, they perform biogeochemical functions that translate into essential services, and regulate global climate. In grazing ecosystems, which represent over 40% of the terrestrial realm, soil microbes respond to aboveground interactions between plants and herbivores. In this thesis, I analyse different aspects of soil microbial functions in the high-altitude grazing ecosystem of the Trans- Himalaya, and quantify some implications for biogeochemical cycles and sustainability under climate change. In particular, I asked two questions, (1) whether land-use change alter the magnitude and heterogeneity of decomposer functions, and (2) whether changes in decomposer biomass follows functional heterogeneity. I found that the extent of human-alteration of the reference state is reflected in the degree of homogenization of decomposer functions. Relative to the native state, magnitude of individual functions was often higher under crops but remained unchanged under livestock, such that land-use had no net effect on multifunctionality. However, univariate and multivariate measures of functional vii heterogeneity were lower under crops but were unaffected under livestock. Stability of decomposer biomass, measured as invariance through time, was comparable across land-use types. These results show that previous knowledge on diversity-relationships in producers and consumers are not easily extended to decomposers, and there are fundamental differences. Although agroecosystems in the Trans-Himalaya show remarkably high degree of ecological resistance, homogenization of their decomposer functions can make them susceptible to environmental fluctuations, such as those foreseen by future climate projections. Overall, this thesis explores and explains how soil microbes contribute to the functioning of grazing ecosystems

Lichen is the poster child for symbiosis, functioning as a collaboration of a fungus and algae or cyanobacteria—or sometimes all three—which enables it to survive in the climatically and nutritionally most challenging environments, such as extreme cold or heat. One of the oldest organisms in earth’s biosphere, it has developed a lifestyle that still retains its mystery but nevertheless provides a paradigm that may serve human societies well: rather than on the competition of individuals it is based on community-building. Displaying a tremendous diversity of colors and shapes, it may paint the landscape, serve as medicine or food, or be used to monitor air quality. Poets marvel at lichen’s power—it can grow into and decompose rock, attach itself to a wide variety of surfaces, and live for thousands of years. Novelists have explored lichen’s extreme longevity for the idea of extending human lifespan and its symbiotic lifestyle as a metaphor for the challenging process of individuation among twins. Today’s appreciation of networks, interconnectivity, and “being-with” may be related to the scientific discovery of symbiotic ways of life as well as an increasing societal awareness of the benefits to be gained from collaboration.

This chapter discusses the essential ecosystem function of microbial decomposition and carrion consumption by scavengers. Decomposers are single-celled, saprophytic or saprozoic organisms, including bacteria, which feed extracellularly on dead material on-site. Scavengers are multicellular organisms, including both invertebrates and vertebrates, which feed on the fragments of carcasses, either on-site or elsewhere. The ecological actions of decomposers and scavengers as elemental recyclers serve to recapture and supply the raw materials that other ecological entities, including plants and consumers, need to maintain the energetic processes of primary and secondary productivity necessary to sustain the long-term continuity of ecological systems. Although many carnivorous vertebrates are facultative scavengers that sometimes feed on carrion, the world's vultures are the only truly obligate vertebrate scavengers, species that feed almost entirely on carrion and that require carrion for their livelihoods.

In this chapter we propose a conceptual framework to guide understanding of the complex nature of the underlying biological processes involved in soil organic carbon (SOC) sequestration. We analyze, step by step, the conditions that promote an accumulation of organic matter in the soil and the maintenance of large SOC stocks. We will focus on the process of soil aggregation, which allows the local creation of conditions unfavorable to microbial activity or disconnection among decomposers and their organic resources, thus contributing to the temporary storage of SOC at different levels of decomposition and different depths in soils. Taking the earthworm drilosphere as an example, we consider the biotic and abiotic factors in their genesis, their diversity and conditions for the stabilization or disaggregation of these structures. We finally discuss the theoretical and technical bottlenecks that impede research providing a clearer understanding, needed to design better management practices that would enhance carbon sequestration in natural and managed ecosystems.

Exciting days lie ahead for paleolimnology. As we embark on a new millennium, the opportunities and challenges in this field are extremely bright. As an epilogue to this book, it seems appropriate to conclude with a few of the developments that seem to me particularly promising for the near future. 1. Increasing application of paleolimnological data to address problems in global climate change. Paleolimnologists need to make governments and societies aware of the importance of high-resolution paleorecords from lakes for providing information about baseline variability of the biosphere, consequences and histories of past climate change events, and past responses of our precious aquatic resources to such changes. Paleolimnology should and will increasingly play a role in providing decision-makers with critical information about earth system history as they formulate policies to cope with these changes. Few, if any, paleoenvironmental records provide earth history records in environments as intimately associated with human activity as lake deposits. Lakes and wetlands are increasingly recognized as potentially important components of the global carbon cycle, especially as environments for sequestering large volumes of carbon, and future research will undoubtedly quantify the magnitude and dynamics of this role. Paleolimnologists will need to work even more closely with climate modelers, hydrologists, and atmospheric scientists in years to come, to insure that the paleorecords we study will help resolve important questions about the earth’s climate system. 2. Advances in geobiology. The rapid developments of new and automated tools in molecular biology and organic geochemistry for analyzing small sample volumes and extracting compound-specific isotopic information from organic compounds have important implications for paleolimnology. In years to come we will increasingly rely on organic geochemistry and microbial geobiology to help decipher the organic record of algal primary producers, decomposers, and other elements of the microbial food web. These are components of a lake’s ecosystem that ecologists recognize as immensely important in biogeochemical cycles and as being on the front line of lake responses to changes in climate and watershed processes, but which have heretofore been largely intractable to any detailed interpretation by paleolimnologists.

Abstract Wastewater is considered a source of water, power, and enriching nutrient for plants. Wastewater treatment is among the most significant biotechnological procedures for treating municipal and industrial sewage across the world. Conventional wastewater treatment methods, however, have constraints, primarily because they are cost-intensive to achieve the aim of wastewater remediation. Microorganisms, on the contrary, outperform humans when it comes to sewage water purification. Their ability to decompose a wide range of organic chemicals and cycle components such as nitrogen, phosphorus, and carbon is unparalleled in ecology. These characteristics have been successfully used in microbial wastewater treatment plants. This chapter discusses the necessity for wastewater treatment, and the function of diverse microbes in wastewater treatment, including new and developing technologies that use microbes for wastewater treatment and purification, such as microbial fuel cells, bioremediation, and activated sludge processes along with the challenges and prospects of using microorganisms in wastewater treatment.

Since the beginning of the industrialization, application of chemical compounds on lands and disposal of contaminants to soil and water systems have caused numerous sorts of alterations in environment, and therefore affected the inhabitant biodiversity. This chapter aims to provide an introduction to bioremediation, an innovative multidisciplinary technology which employs microorganisms in order to reduce, eliminate, contain or transform hazardous contaminants in soil, sediment or water. So far, microorganisms and plants have been utilized to breakdown or transform several contaminants into less toxic forms. Main focus of chapter will be on several bioremediation techniques, employing indigenous microorganisms to decompose biodegradable pollutants in order to stabilize or to transform the contaminants into non-hazardous by-products. Besides, it will elucidate several factors effecting bioremediation process, involving energy source as a dominant necessity of microbial activity. Undoubtedly, bioremediation offers a greener pathway of remediation in comparison with wide varieties of conventional and artificial treatments.

Abstract Soils are an integral part of the tallgrass prairie ecosystem. Jenny (1941) suggested that soil formation results from multiple factors: climate, organisms, topography, and parent material, all interacting over time. In the tallgrass prairie-soils ecosystem, the prairie vegetation has exerted great influence on soil formation, but the physical and chemical properties of soil also affect the kinds, amount, and spatial distribution of the vegetation. The relationships between soils and the biota of the prairie are extremely complex The soil biota in tallgrass prairie represents a diversity of genetic and physiological traits. Although the aboveground flora and fauna often characterize the prairie, the biomass of the soil biota can be of the same order of magnitude as the visible portion of the prairie (Paul et al. 1979). This invisible prairie is responsible for much of the energy flow and nutrient cycling (Chapters 13 and 14, this volume) in the prairie and contributes to the development of soils. Although some soil organisms use sunlight or inorganic substrates to obtain energy, a vast majority of the soil biota are heterotrophs, using organic compounds to obtain their energy. Photosynthetically fixed C produced by plants decomposes, supporting the microbial community. The ecology and diversity of the soil biota of tallgrass prairie remain relatively unexplored despite its importance in decomposition and nutrient cycling (Clark and Paul 1970; Seastedt et al. 1988a; Seastedt and Hayes 1988).

In nature, lactic acid bacteria (LAB) are the predominant microflora of milk and its products. LAB is a diverse group of phylogenetically related microbes that produce lactic acid as the primary byproduct of carbohydrate fermentation. The fermented food sector extensively uses LAB, which can ferment carbohydrates to generate lactic acid. LAB’s microbial metabolic characteristics have drawn more attention due to their significant function in the food industry and their probiotic properties. LAB can decompose food macromolecules, break down indigestible polysaccharides, and generate a wide range of products during metabolism, including exopolysaccharides, bacteriocins, short-chain fatty acids, vitamins and amines. LAB is employed to enhance the flavour of fermented foods, boost food nutrition, lessen dangerous chemicals, lengthen shelf life, and be utilized as probiotics to improve bodily wellness. The name “probiotics” or “pro-life” was coined due to LAB’s ability to prevent and treat various illnesses. Since LAB can maintain food stability and safety for decades, it has been thoroughly investigated for bio-preservation. Numerous genera found in LAB produce metabolites that have been approved for use in food by various food regulatory organizations. LAB are considered safe organisms with the designation of GRAS (generally recognized as safe) and have relatively basic metabolic pathways that are fairly amenable to changes. The recent studies of metabolites produced from LAB, their potential and their use in food applications are discussed.

The surfaces of building materials of hydrotechnical constructions undergo the process of algae biofouling. The degree of damage depends on the environmental factors that are affect-ed by the level of anthropogenic load areas. Modeling the biofouling process of concrete with algae under laboratory conditions has allowed determining their impact on the building ma-terial, accompanied by changes in chemical and mineralogical composition of the surface of products. The microscopic examination of sample’s surfaces and evaluation of the effective-ness of various ions leaching from building materials shows the results of "algal attack" relat-ed to the acceleration of biodegradation of materials under the influence of aggressive meta-bolic products, mechanical action neoplasms, creating optimal conditions for the development of subsequent aerobic microbial decomposers. To clarify the nature of chemical processes in the system “algocenosis – concrete” the changes of chemical and phase (mineralogical) com-position of the surface layer of concrete sample were studied. The effect that algae produce on hydraulic engineering constructions is due to the fact that these organisms, belonging to phototrophs and standing at the beginning of the food chain, initiate new microbial growth.

The surfaces of building materials of hydrotechnical constructions undergo the process of algae biofouling. The degree of damage depends on the environmental factors that are affect-ed by the level of anthropogenic load areas. Modeling the biofouling process of concrete with algae under laboratory conditions has allowed determining their impact on the building ma-terial, accompanied by changes in chemical and mineralogical composition of the surface of products. The microscopic examination of sample’s surfaces and evaluation of the effective-ness of various ions leaching from building materials shows the results of "algal attack" relat-ed to the acceleration of biodegradation of materials under the influence of aggressive meta-bolic products, mechanical action neoplasms, creating optimal conditions for the development of subsequent aerobic microbial decomposers. To clarify the nature of chemical processes in the system “algocenosis – concrete” the changes of chemical and phase (mineralogical) com-position of the surface layer of concrete sample were studied. The effect that algae produce on hydraulic engineering constructions is due to the fact that these organisms, belonging to phototrophs and standing at the beginning of the food chain, initiate new microbial growth.

Camel milk is an important source of nutrients such as proteins and vitamins, including whey proteins, which make inhibition of oil oxidation and microbial growth. The proteolytic have high antioxidant activity due to their amino acid content. The antioxidant properties of camel milk are also attributed to the structural composition of whey proteins upon hydrolysis and their content of bioactive peptides that have antioxidant activities. According to the study, the decomposers showed a high activity in their ability to capture the DPPH radical and bind the ferric ion amounted to 53.19% and 62.88%, respectively, at a concentration of 20 mg/ml, in addition to having a high reducing capacity of 77.199% at the same concentration, and their amino acid content was estimated. The hydrolysates’ contribution for enhancing the storage capacity of the oils was studied by decreasing the peroxide number values of sesame seed oil stored at laboratory temperature for 60 days

Many oilfields such as supergiant Romaschkinskoye oilfield in Russia contain heavy oils that are complicated to recover. In order to increase the proportion of obtained oil, methods of enhanced oil recovery are implemented, and microbial methods (MEOR) are considered as safe and efficient once. In-situ MEOR are based on stimulation of oilwell microflora that partly decomposes hydrocarbon molecules or alters oil-water interface tension. Despite oilwells are an environments with anaerobic conditions, many allochtonous microbes there are able to use aerobic pathways. Moreover, stimulation of those aerobic microbes by addition of nutrients and oxygen (that is contained in the production water) results in significant oil recovery increase since aerobes produce metabolites that activate the microflora of the lower anaerobic zone. However, aerobic microbial communities of many oilwells remain unstudied and their role for oil recovery is underestimated. The purpose of the present study was to reveal the biodiversity and oil-emulsifying ability of the aerobic microorganisms inhabiting heavy oils from the supergiant Romaschkinskoye oilfield. For this purpose, oil was sampled from 5 oil reservoirs belonging to the Romaschkinskoye oilfield. For each reservoir, oil was obtained from 3 different wells recovering oil from different depths. After cultivation under aerobic conditions, 16 isolates belonging to Bacillus and Enterococcus genera were obtained from the samples. The emulsification index (E24) revealed for cultural media of those isolates ranged between 15 and 70%. For six isolates, it exceeded 60% which can be promising for using MEOR. Further investigation of the ability of those isolates to stimulate the oil anaerobic microflora is required.

To identify microorganisms that can penetrate into the endophytic niche of the grain of barley plants, many years of vegetative experiments were conducted on sod-podzolic soil without the use of mineral fertilizers. In the non-growing season, a biological product, consisting of cellulolytic association of bacteria with genotypic passport, decomposed barley straw. Presowing treatment of seeds was not carried out, therefore, during the growing season; local microorganisms decomposing plant residues could be present in the barley rhizosphere. After six years of rotation of barley plants, the microbiological composition of its seed niche was studied. As a result, it was found that in the seeds of barley bacteria are present in an amount of 240 ± 20 CFU/g of grain. Isolated pure cultures of microorganisms were identified as Cellulomonas gelida, Micrococcus luteus and Bacillus licheniformis by the sequence of ITS fragments of 16S rRNA. These types of bacteria were also present in the used biological product. Based on the research conducted, it can be assumed, that permanent cultivation of barley plants and sowing of seeds of the previous year can contribute to the formation of effective microbial and plant biosystems that are resistant to environmental stress.

Abstract Polyacrylamide-based friction reducer is commonly used in well completion for unconventional reservoirs. However, residual polymer trapped in the near well-bore region could create unintended flow restrictions and could negatively impact oil production. An eco-friendly approach to regain conductivity was developed by stimulating indigenous bacteria for residual polymer biodegradation. In this work, a series of laboratory experiments were conducted using produced water and oil from Permian Basin, polyacrylamide-based polymer, and a modified nutrient recipe that contained 100 to 300 ppm of inorganic salts. The sealed sample vials containing water, oil, and polymer were prepared in a sterilized anaerobic chamber and then kept in a 160° F incubator to simulate the reservoir condition. Feasibility tests of bacteria growth and biodegradation evaluation of polymer were conducted using an optical laser microscopic system with bacteria tagged with fluorescent dye. Size regression was calculated and applied to a mathematical model based on actual fracture aperture distribution data from shale formation. The indigenous bacteria were successfully stimulated with and without the existence of the friction reducer. It was observed that the size of polymer particles decreased from over 300 µm to less than 20 µm after 15 days. Under the condition of produced water injection, 140° F reservoir temperature, and anaerobic environment, about 30% of the natural fractures in shale were calculated to be damaged and remediated within 15 days. This work is a pioneer research on microbial EOR application in unconventional reservoirs with only indigenous bacteria involved. In field applications, only an extremely low amount of nutrient is required in this process which provides great economic potential. Additionally, the nutrients introduced into the reservoirs will be fully consumed by bacteria during treatment, and the bacteria will be decomposed into organic molecules soon after the treatment. Thus, this technique is environmental- and economical- friendly for the purpose of polymer damage remediation to maximize the recoverable.