Microbial responses to changes in land use

Background/Question/Methods
Land use change is one of the greatest threats to biodiversity worldwide. This is especially true for land use change that results in the destruction of intact forest, or "deforestation”. Deforestation is causing a loss of biological diversity on an unprecedented scale, especially in the Tropics. It is unclear how the majority of the biodiversity on Earth – microbial biodiversity – is responding to these extraordinary rates of deforestation. I will provide an overview of our current understanding of microbial responses to deforestation. I will focus, as an example, on our current research regarding the effects of deforestation on the diversity of arbuscular mycorrhizal fungi (AMF), bacteria and archaea within Amazon Rainforest soils. This study takes advantage of an established chronosequence of primary rainforest, pastures of various ages, and secondary rainforest to determine the effect of deforestation on the taxonomic, phylogenetic and functional diversity of soil microorganisms, assayed using culture-independent methods.

Results/Conclusions
There is increasing evidence that deforestation significantly affects microbial diversity, and that “recovery” of microbial diversity in secondary forest soils is incomplete. For example, rarefaction curves suggest that the accumulation of AMF taxa is higher for Amazon primary forest soil relative to secondary forest soil. In addition, the community composition varies with land use; three AMF taxa were shared between primary and secondary forests, seven were found only in primary forest, and three were found exclusively in secondary forest soil. We also observed that the phylogenetic diversity of AMF is more reduced in secondary forest soils than expected given the regional pool of AMF taxa.

*The audio track for talks in this symposium may be obtained at the following web address:*

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Sterols and fecal indicator microorganisms in sediments from Admiralty Bay, Antarctica

Amostras de sedimento, coletadas nas proximidades da saída de esgoto da Estação Antártica Comandante Ferraz (Brasil), Antártica, foram medidos durante o verão de 1999/2000. As concentrações de esteróis totais e coprostanol variaram entre 0,09 e 19,6 ¼g.g-1 e < 0,01 e 14,0 ¼g.g-1 de sedimento seco. Nossas análises mostraram que apenas os pontos localizados até 400 m desde a saída de esgotos apresentaram contribuições provenientes do esgoto da estação brasileira. Baixos níveis de coprostanol e alta concentração de colesterol em pontos distantes puderam ser atribuídos a fontes naturais, como os mamíferos marinhos e organismos planctônicos. Indicadores microbiológicos (E. coli, streptococci fecais e Clostridium perfringens) não foram detectados até 50 m desde a saída de esgotos. Ambos indicadores de poluição fecal produziram dados consistentes, embora os esteróis fecais tenham sido mais apropriados para avaliar quantidades traço de material fecal. Este estudo concluiu que a contaminação por esgotos está limitada apenas aos pontos mais próximos da saída de esgoto. Em geral, as concentrações de esteróis fecais e indicadores microbiológicos foram menores do que em outras regiões antárticas e centros urbanos.Sediments from the proximity of Ferraz station outfall, located in Admiralty Bay, Antarctica, were analyzed for fecal indicator microorganisms and sterols during the austral summer of 1999/2000 in order to assess human sewage input. Concentrations of total sterols and coprostanol ranged from 0.09 to 19.6 ¼g.g-1 and < 0.01 and 14.0 ¼g.g-1 dry weight (dw), respectively. Our analyses indicated that only sites within to 400m of the sewage outfall exhibited a sterol signal characteristic of human sewage input. Low levels of coprostanol and high levels of cholesterol in distant sites could be attributed to natural sources such as marine mammals and planktonic organisms. Fecal indicator microorganisms (E. coli, fecal streptococci and Clostridium perfringens) were non-detectable beyond 50m from outfall. Both indicators (sterols and fecal indicator microorganisms) produced consistent data and fecal sterol parameters have sho wn themselves to be efficient in the evaluation of trace amounts of fecal material. This study concluded that sewage contamination is limited to the immediate vicinity of the sewage outfall. In general, the concentration of fecal sterols and microbiological indicators were lower than in other Antarctic areas

Biotransformacija supstituiranih feniletanola i acetofenona s pomoću bakterija iz okoliša

Whole cells of hydrocarbon-degrading bacteria, isolated from polluted sediments in the Santos Estuary (Baixada Santista, São Paulo, Brazil), were able to catalyse oxidoreduction reactions with various substituted phenylethanols and acetophenones as substrates. A number of substituted phenylethanols were formed with high (>99 %) enantiomeric excess. The results of microbial oxidation of phenylethanols 2, 3, 5–7 by Acinetobacter sp. 6.4T and the reduction of acetophenones 1a–6a by Serratia marcescens 5.4T showed that the bacteria used as biocatalysts in this study present significant potential for exploitation in biotechnological processes. The reduction of prochiral acetophenones by Serratia marcescens 3.5T yielded optically active alcohols with 90–99 % enantiomeric excess, and Acinetobacter sp. 6.4T is a potential biocatalyst for the oxidation of alcohols.Cijele stanice bakterija koje razgrađuju vodik, izolirane iz onečišćenih sedimenata iz zaljeva Santos (Baixada Santista, São Paulo, Brazil), upotrijebljene su kao katalizatori oksidacije i redukcije raznih supstituiranih feniletanola i acetofenona. Brojni supstituirani feniletanoli nastali su u velikom enantiomernom višku (>99 %). Rezultati mikrobne oksidacije feniletanola 2, 3, 5-7 s pomoću bakterijskog soja Acinetobacter sp. 6,4T i redukcije acetofenona 1a-6a s pomoću soja Serratia marcescens 5,4T pokazali su da postoji velika mogućnost njihove primjene u biotehnološkim procesima. Redukcijom prokiralnih acetofenona s pomoću soja Serratia marcescens 3,5T nastali su optički aktivni alkoholi u enantiomernom višku od 90 do 99 %, te je utvrđeno da je soj Acinetobacter sp. 6,4T jak biokatalizator oksidacije alkohola

Fungal diversity in deep-sea sediments associated with asphalt seeps at the Sao Paulo Plateau

We investigated the fungal diversity in a total of 20 deep-sea sediment samples (of which 14 samples were associated with natural asphalt seeps and 6 samples were not associated) collected from two different sites at the Sao Paulo Plateau off Brazil by Ion Torrent PGM targeting ITS region of ribosomal RNA. Our results suggest that diverse fungi (113 operational taxonomic units (OTUs) based on clustering at 97% sequence similarity assigned into 9 classes and 31 genus) are present in deep-sea sediment samples collected at the Sao Paulo Plateau, dominated by Ascomycota (74.3%), followed by Basidiomycota (11.5%), unidentified fungi (7.1%), and sequences with no affiliation to any organisms in the public database (7.1%). However, it was revealed that only three species, namely Penicillium sp., Cadophora malorum and Rhodosporidiwn diobovatum, were dominant, with the majority of OTUs remaining a minor community. Unexpectedly, there was no significant difference in major fungal community structure between the asphalt seep and non-asphalt seep sites, despite the presence of mass hydrocarbon deposits and the high amount of macro organisms surrounding the asphalt seeps. However, there were some differences in the minor fungal communities, with possible asphalt degrading fungi present specifically in the asphalt seep sites. In contrast, some differences were found between the two different sampling sites. Classification of OTUs revealed that only 47 (41.6%) fungal OTUs exhibited >97% sequence similarity, in comparison with pre-existing ITS sequences in public databases, indicating that a majority of deep-sea inhabiting fungal taxa still remain undescribed. Although our knowledge on fungi and their role in deep-sea environments is still limited and scarce, this study increases our understanding of fungal diversity and community structure in deep-sea environments.Japan Society for the Promotion of ScienceJapan Agcy Marine Earth Sci & Technol, 2-15 Natsushima Cho, Yokosuka, Kanagawa 2370061, JapanUniv Vale Itajal, Dept Biol Sci, CTTMar, R Uruguai 458, BR-88302202 Itajal, SC, BrazilUniv Fed Sao Paulo, Rua Prof Artur Riedel 275, BR-09972270 Diadema, SP, BrazilUniv Sao Paulo, Inst Oceanog, 191 Praca Oceanog, BR-05508120 Sao Paulo, SP, BrazilUniv Fed Sao Paulo, Rua Prof Artur Riedel 275, BR-09972270 Diadema, SP, BrazilJSPS: 23770098JSPS: 15K18601Web of Scienc

High Prevalence of Gammaproteobacteria in the Sediments of Admiralty Bay and North Bransfield Basin, Northwestern Antarctic Peninsula

Microorganisms dominate most Antarctic marine ecosystems, in terms of biomass and taxonomic diversity, and play crucial role in ecosystem functioning due to their high metabolic plasticity. Admiralty Bay is the largest bay on King George Island (South Shetland Islands, Antarctic Peninsula) and a combination of hydro-oceanographic characteristics (bathymetry, sea ice and glacier melting, seasonal entrance of water masses, turbidity, vertical fluxes) create conditions favoring organic carbon deposition on the seafloor and microbial activities. We sampled surface sediments from 15 sites across Admiralty Bay (100502 m total depth) and the adjacent North Bransfield Basin (6931147 m), and used the amplicon 454-sequencing of 16S rRNA gene tags to compare the bacterial composition, diversity, and microbial community structure across environmental parameters (sediment grain size, pigments and organic nutrients) between the two areas. Marine sediments had a high abundance of heterotrophic Gammaproteobacteria (92.4% and 83.8% inside and outside the bay, respectively), followed by Alphaproteobacteria (2.5 and 5.5%), Firmicutes (1.5 and 1.6%), Bacteroidetes (1.1 and 1.7%), Deltaproteobacteria (0.8 and 2.5%) and Actinobacteria (0.7 and 1.3%). Differences in alpha-diversity and bacterial community structure were found between the two areas, reflecting the physical and chemical differences in the sediments, and the organic matter input.Brazilian National Council for Scientific and Technological Development - CNPq (MABIREH/IPY/CAML)CAPES-Master's fellowshipUniv Sao Paulo, Inst Oceanog, Dept Oceanog Biol, Sao Paulo, BrazilUniv Fed Santa Catarina, Ctr Ciencias Biol, Florianopolis, SC, BrazilUniv Fed Sao Paulo, Inst Ciencias Ambientais Quim & Farmaceut, Dept Ciencias Ambientais, Diadema, BrazilUniv Fed Rio de Janeiro, Inst Biol, Dept Zool, Rio De Janeiro, BrazilUniv Fed Sao Paulo, Inst Ciencias Ambientais Quim & Farmaceut, Dept Ciencias Ambientais, Diadema, BrazilCNPq (MABIREH/IPY/CAML): 520293/2006-1Web of Scienc

Biotransformacija supstituiranih feniletanola i acetofenona s pomoću bakterija iz okoliša

Whole cells of hydrocarbon-degrading bacteria, isolated from polluted sediments in the Santos Estuary (Baixada Santista, São Paulo, Brazil), were able to catalyse oxidoreduction reactions with various substituted phenylethanols and acetophenones as substrates. A number of substituted phenylethanols were formed with high (>99 %) enantiomeric excess. The results of microbial oxidation of phenylethanols 2, 3, 5–7 by Acinetobacter sp. 6.4T and the reduction of acetophenones 1a–6a by Serratia marcescens 5.4T showed that the bacteria used as biocatalysts in this study present significant potential for exploitation in biotechnological processes. The reduction of prochiral acetophenones by Serratia marcescens 3.5T yielded optically active alcohols with 90–99 % enantiomeric excess, and Acinetobacter sp. 6.4T is a potential biocatalyst for the oxidation of alcohols.Cijele stanice bakterija koje razgrađuju vodik, izolirane iz onečišćenih sedimenata iz zaljeva Santos (Baixada Santista, São Paulo, Brazil), upotrijebljene su kao katalizatori oksidacije i redukcije raznih supstituiranih feniletanola i acetofenona. Brojni supstituirani feniletanoli nastali su u velikom enantiomernom višku (>99 %). Rezultati mikrobne oksidacije feniletanola 2, 3, 5-7 s pomoću bakterijskog soja Acinetobacter sp. 6,4T i redukcije acetofenona 1a-6a s pomoću soja Serratia marcescens 5,4T pokazali su da postoji velika mogućnost njihove primjene u biotehnološkim procesima. Redukcijom prokiralnih acetofenona s pomoću soja Serratia marcescens 3,5T nastali su optički aktivni alkoholi u enantiomernom višku od 90 do 99 %, te je utvrđeno da je soj Acinetobacter sp. 6,4T jak biokatalizator oksidacije alkohola

Effect ofplankton-derivedorganic matter on themicrobial community of coastal marine sediments

An experimental study was carried out to observe the microbial response to two different plankton-derived organic matter inputs in a coastal sedimentary community of Ubatuba, São Paulo, SE Brazil. The organic enrichment experiment was conducted in order to test experimentally the stimulus of the sediment prokaryotic community after the input of labile material simulating an algal bloom reaching the sea floor. A total of 57 corers (two treatments: the diatom Phaeodactylum tricornutun and the phyto flagellate Tetraselmis sp. and a control) were maintained for a total of 30 days in constant temperature, circulation and oxygenation. After the addition of algae an increase in oxygen consumption was observed, accompanied by an increase of prokaryotic total and live density, showing an immediate response from the community to the input of labile material in the sediment. Analyses of molecular fingerprints of bacterial communities by denaturing gel gradien electrophoresis (DGGE) showed differences in bacterial community composition between both treatments and control just after algae addition. This was well evidenced after bacteria genomic libraries analyses that showed differences in diversity and dominance between treatments. In general, Gammaproteobacteria was the most diverse and abundant grouping the sediment samples. However, the addition of phytoflagellates led to as hiftin dominance in favor of Alphaproteobacteria while diatom input led to a greater bacterial diversit

Microbial diversity of deep-sea ferromanganese crust field in the Rio Grande Rise, Southwestern Atlantic Ocean

Seamounts are often covered with Fe and Mn oxides, known as ferromanganese (Fe–Mn) crusts. Future mining of these crusts is predicted to have significant effects on biodiversity in mined areas. Although microorganisms have been reported on Fe–Mn crusts, little is known about the role of crusts in shaping microbial communities. Here, we investigated microbial communities based on 16S rRNA gene sequences retrieved from Fe–Mn crusts, coral skeleton, calcarenite, and biofilm at crusts of the Rio Grande Rise (RGR). RGR is a prominent topographic feature in the deep southwestern Atlantic Ocean with Fe–Mn crusts. Our results revealed that crust field of the RGR harbors a usual deep-sea microbiome. No differences were observed on microbial community diversity among Fe–Mn substrates. Bacterial and archaeal groups related to oxidation of nitrogen compounds, such as Nitrospirae, Nitrospinae phyla, Candidatus Nitrosopumilus within Thaumarchaeota group, were present on those substrates. Additionally, we detected abundant assemblages belonging to methane oxidation, i.e., Methylomirabilales (NC10) and SAR324 (Deltaproteobacteria). The chemolithoautotrophs associated with ammonia-oxidizing archaea and nitrite-oxidizing bacteria potentially play an important role as primary producers in the Fe–Mn substrates from RGR. These results provide the first insights into the microbial diversity and potential ecological processes in Fe–Mn substrates from the Atlantic Ocean. This may also support draft regulations for deep-sea mining in the region

Spatial patterns of microbial diversity in Fe-Mn deposits and associated sediments in the Atlantic and Pacific oceans

Mining of deep-sea Fe-Mn deposits will remove crusts and nodules from the seafloor. The growth of these minerals takes millions of years, yet little is known about their microbiome. Besides being key elements of the biogeochemical cycles and essential links of food and energy to deep-sea, microbes have been identified to affect manganese oxide formation. In this study, we determined the composition and diversity of Bacteria and Archaea in deep-sea Fe-Mn crusts, nodules, and associated sediments from two areas in the Atlantic Ocean, the Tropic Seamount and the Rio Grande Rise. Samples were collected using ROV and dredge in 2016 and 2018 oceanographic campaigns, and the 16S rRNA gene was sequenced using Illumina platform. Additionally, we compared our results with microbiome data of Fe-Mn crusts, nodules, and sediments from Clarion-Clipperton Zone and Takuyo-Daigo Seamount in the Pacific Ocean. We found that Atlantic seamounts harbor an unusual and unknown Fe-Mn deposit microbiome with lower diversity and richness compared to Pacific areas. Crusts and nodules from Atlantic seamounts have unique taxa (Alteromonadales, Nitrospira, and Magnetospiraceae) and a higher abundance of potential metal-cycling bacteria, such as Betaproteobacteriales and Pseudomonadales. The microbial beta-diversity from Atlantic seamounts was clearly grouped into microhabitats according to sediments, crusts, nodules, and geochemistry. Despite the time scale of million years for these deposits to grow, a combination of environmental settings played a significant role in shaping the microbiome of crusts and nodules. Our results suggest that microbes of Fe-Mn deposits are key in biogeochemical reactions in deep-sea ecosystems. These findings demonstrate the importance of microbial community analysis in environmental baseline studies for areas within the potential of deep-sea mining