scholarly journals Quaternary nannoplankton in the Northeast Java Basin

2021 ◽  
Vol 47 (3) ◽  
pp. 43-49
Author(s):  
Rubiyanto Kapid ◽  
Wahyu Dwijo Santoso ◽  
Halmi Insani
Keyword(s):  
Marine Sediments ◽  
Marine Sediment ◽  
Late Miocene ◽  
Age Estimation ◽  
Field Of View ◽  
Quaternary Sediment

In Indonesia, nannofosils are commonly used for age estimation on Miocene marine sediment, but they are rarely performed on Quaternary sediment. This paper introduces two nannofossil biozones, Martini (1971) and Backman et al. (2012) and the comparison between the two biozones. An uninterrupted interval of marine sediments was described and picked for quantitative nannoplankton analysis. The samples were taken from Ledok Formation to Lidah Formation in Pati Region, Northeast Java Basin. The samples were prepared by quick smear slides method and and analyzed by quantitative field of view method. Martini (1971) biozone can be used to subdivide the Late Miocene–Pleistocene sediments into 5 biozones, but Backman et al. (2012) can be used to classify the same sediments into 8 biozones. The biozone subdivision from Backman et al. (2012) is more detailed than that of Martini (1971) because an updated dating and biozone in the three new dating zone data.

scholarly journals Anaerobic bacterial degradation of protein and lipid macromolecules in subarctic marine sediment

2020 ◽  
Author(s):  
Claus Pelikan ◽  
Kenneth Wasmund ◽  
Clemens Glombitza ◽  
Bela Hausmann ◽  
Craig W. Herbold ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Marine Sediment ◽  
Volatile Fatty Acids ◽  
Degradation Products ◽  
Stable Isotope Probing ◽  
Bacterial Degradation ◽  
Rrna Gene ◽  
Genomic Features ◽  
Carbon Processing

AbstractMicroorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet the taxonomic identities of microorganisms that actively degrade them remain poorly resolved. Here, we revealed identities, trophic interactions, and genomic features of bacteria that degraded 13C-labeled proteins and lipids in cold anoxic microcosms containing sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within 5 days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within 10 days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas species are prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides new insights into the identities, functions, and genomes of bacteria that actively degrade abundant necromass macromolecules in the seafloor.

scholarly journals Multiple strain analysis of Streptomyces species from Philippine marine sediments reveals intraspecies heterogeneity in antibiotic activities

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Chuckcris P. Tenebro ◽  
Dana Joanne Von L. Trono ◽  
Carmela Vannette B. Vicera ◽  
Edna M. Sabido ◽  
Jovito A. Ysulat ◽  
...  
Keyword(s):  
16S Rrna ◽  
Marine Sediments ◽  
Marine Sediment ◽  
Antibiotic Production ◽  
Marine Ecosystem ◽  
Strain Analysis ◽  
Antibacterial Activities ◽  
Antibiotic Activity ◽  
Ecological Niches ◽  
Streptomyces Species

AbstractThe marine ecosystem has become the hotspot for finding antibiotic-producing actinomycetes across the globe. Although marine-derived actinomycetes display strain-level genomic and chemodiversity, it is unclear whether functional traits, i.e., antibiotic activity, vary in near-identical Streptomyces species. Here, we report culture-dependent isolation, antibiotic activity, phylogeny, biodiversity, abundance, and distribution of Streptomyces isolated from marine sediments across the west-central Philippines. Out of 2212 marine sediment-derived actinomycete strains isolated from 11 geographical sites, 92 strains exhibited antibacterial activities against multidrug-resistant Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. The 16S rRNA and rpoB gene sequence analyses confirmed that antibiotic-producing strains belong to the genus Streptomyces, highlighting Streptomyces parvulus as the most dominant species and three possible new species. Antibiotic-producing Streptomyces strains were highly diverse in Southern Antique, and species diversity increase with marine sediment depth. Multiple strains with near-identical 16S rRNA and rpoB gene sequences displayed varying strength of antibiotic activities. The genotyping of PKS and NRPS genes revealed that closely related antibiotic-producing strains have similar BGC domains supported by their close phylogenetic proximity. These findings collectively suggest Streptomyces' intraspecies adaptive characteristics in distinct ecological niches that resulted in outcompeting other bacteria through differential antibiotic production.

scholarly journals Isolation of Broad-Host-Range Replicons from Marine Sediment Bacteria

1998 ◽  
Vol 64 (8) ◽  
pp. 2822-2830 ◽  
Author(s):  
Patricia A. Sobecky ◽  
Tracy J. Mincer ◽  
Michelle C. Chang ◽  
Aresa Toukdarian ◽  
Donald R. Helinski
Keyword(s):  
Sequence Analysis ◽  
Marine Sediments ◽  
Marine Sediment ◽  
Replication Initiation ◽  
Plasmid Replication ◽  
Broad Host Range ◽  
Bacterial Isolates ◽  
Replication Origins ◽  
Naturally Occurring ◽  
Sediment Bacteria

ABSTRACT Naturally occurring plasmids isolated from heterotrophic bacterial isolates originating from coastal California marine sediments were characterized by analyzing their incompatibility and replication properties. Previously, we reported on the lack of DNA homology between plasmids from the culturable bacterial population of marine sediments and the replicon probes specific for a number of well-characterized incompatibility and replication groups (P. A. Sobecky, T. J. Mincer, M. C. Chang, and D. R. Helinski, Appl. Environ. Microbiol. 63:888–895, 1997). In the present study we isolated 1.8- to 2.3-kb fragments that contain functional replication origins from one relatively large (30-kb) and three small (<10-kb) naturally occurring plasmids present in different marine isolates. 16S rRNA sequence analyses indicated that the four plasmid-bearing marine isolates belonged to the α and γ subclasses of the classProteobacteria. Three of the marine sediment isolates are related to the γ-3 subclass organisms Vibrio splendidusand Vibrio fischeri, while the fourth isolate may be related to Roseobacter litoralis. Sequence analysis of the plasmid replication regions revealed the presence of features common to replication origins of well-characterized plasmids from clinical bacterial isolates, suggesting that there may be similar mechanisms for plasmid replication initiation in the indigenous plasmids of gram-negative marine sediment bacteria. In addition to replication inEscherichia coli DH5α and C2110, the host ranges of the plasmid replicons, designated repSD41, repSD121, repSD164, and repSD172, extended to marine species belonging to the generaAchromobacter, Pseudomonas,Serratia, and Vibrio. While sequence analysis of repSD41 and repSD121 revealed considerable stretches of homology between the two fragments, these regions do not display incompatibility properties against each other. The replication origin repSD41 was detected in 5% of the culturable plasmid-bearing marine sediment bacterial isolates, whereas the replication origins repSD164 and repSD172 were not detected in any plasmid-bearing bacteria other than the parental isolates. Microbial community DNA extracted from samples collected in November 1995 and June 1997 and amplified by PCR yielded positive signals when they were hybridized with probes specific for repSD41 and repSD172 replication sequences. In contrast, replication sequences specific for repSD164 were not detected in the DNA extracted from marine sediment microbial communities.

scholarly journals Transport of branched tetraether lipids from the Tagus River basin to the coastal ocean of the Portuguese margin: consequences for the interpretation of the MBT'/CBT paleothermometer

2014 ◽  
Vol 11 (3) ◽  
pp. 3731-3776 ◽  
Author(s):  
C. Zell ◽  
J.-H. Kim ◽  
M. Balsinha ◽  
D. Dorhout ◽  
C. Fernandes ◽  
...  
Keyword(s):  
River Basin ◽  
Marine Sediments ◽  
Marine Sediment ◽  
Drainage Basin ◽  
River System ◽  
Coastal Marine ◽  
Source To Sink ◽  
Tagus River ◽  
In Situ Production

Abstract. Branched glycerol dialkyl glycerol tetraethers (brGDGTs), which are transported from soil to marine sediment by rivers, have been used to reconstruct the mean annual air temperature (MAAT) and soil pH of the drainage basin using the methylation index of branched tetraethers (MBT, recently refined as MBT') and cyclization index of branched tetraethers (CBT) from coastal marine sediment records. In this study we are tracing the brGDGTs from source to sink in the Tagus River basin, the longest river system on the Iberian Peninsula, by determining their concentration and distribution in soils, river suspended particulate matter (SPM), riverbank sediments, marine SPM, and marine surface sediments. The concentrations of brGDGTs in river SPM were substantially higher and their distributions were different compared to those of the drainage basin soils. This indicates that brGDGTs are mainly produced in the river itself. In the marine environment, the brGDGT concentrations rapidly decreased with increasing distance from the Tagus estuary. At the same time, the brGDGT distributions in marine sediments also changed, indicating that marine in-situ production also takes place. These results show that there are various problems that complicate the use of the MBT'/CBT for paleoreconstructions using coastal marine sediments in the vicinity of a river. However, if the majority of brGDGTs are produced in the river, it might be possible to reconstruct the environmental (temperature and pH) conditions of the river water using appropriate aquatic calibrations, provided that marine core locations are chosen in such a way that the brGDGTs in their sediments are predominantly derived from riverine in-situ production.

scholarly journals Comparison of the Levels of Bacterial Diversity in Freshwater, Intertidal Wetland, and Marine Sediments by Using Millions of Illumina Tags

2012 ◽  
Vol 78 (23) ◽  
pp. 8264-8271 ◽  
Author(s):  
Yu Wang ◽  
Hua-Fang Sheng ◽  
Yan He ◽  
Jin-Ya Wu ◽  
Yun-Xia Jiang ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Marine Sediment ◽  
Bacterial Communities ◽  
Principal Component ◽  
Freshwater Sediment ◽  
Intertidal Sediment ◽  
Taxon Richness ◽  
Natural Sediment ◽  
Content Type ◽  
Intertidal Wetland

ABSTRACTSediment, a special realm in aquatic environments, has high microbial diversity. While there are numerous reports about the microbial community in marine sediment, freshwater and intertidal sediment communities have been overlooked. The present study determined millions of Illumina reads for a comparison of bacterial communities in freshwater, intertidal wetland, and marine sediments along Pearl River, China, using a technically consistent approach. Our results show that both taxon richness and evenness were the highest in freshwater sediment, medium in intertidal sediment, and lowest in marine sediment. The high number of sequences allowed the determination of a wide variety of bacterial lineages in all sediments for reliable statistical analyses. Principal component analysis showed that the three types of communities could be well separated from phylum to operational taxonomy unit (OTU) levels, and the OTUs from abundant to rare showed satisfactory resolutions. Statistical analysis (LEfSe) demonstrated that the freshwater sediment was enriched withAcidobacteria,Nitrospira,Verrucomicrobia,Alphaproteobacteria, andBetaproteobacteria. The intertidal sediment had a unique community with diverse primary producers (such asChloroflexi,Bacillariophyta,Gammaproteobacteria, andEpsilonproteobacteria) as well as saprophytic microbes (such asActinomycetales,Bacteroidetes, andFirmicutes). The marine sediment had a higher abundance ofGammaproteobacteriaandDeltaproteobacteria, which were mainly involved in sulfate reduction in anaerobic conditions. These results are helpful for a systematic understanding of bacterial communities in natural sediment environments.

scholarly journals Paleomagnetic and paleoenvironmental implications of magnetofossil occurrences in late Miocene marine sediments from the Guadalquivir Basin, SW Spain

2014 ◽  
Vol 5 ◽  
Author(s):  
Juan C. Larrasoaña ◽  
Qingsong Liu ◽  
Pengxiang Hu ◽  
Andrew P. Roberts ◽  
Pilar Mata ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Late Miocene ◽  
Sw Spain

On the presence of regular periodicities in the thermoluminescence profile of a recent sea sediment core

1990 ◽  
Vol 330 (1615) ◽  
pp. 481-486 ◽  
Keyword(s):  
Solar Activity ◽  
Tree Ring ◽  
Sediment Core ◽  
Marine Sediments ◽  
Marine Sediment ◽  
Environmental Conditions ◽  
Dominant Role ◽  
Solar Variability ◽  
Entire Period ◽  
The Past

We briefly discuss how the thermoluminescence (TL) profile of a young marine sediment provides phenomenological information on the changes in the environmental conditions in the past 18 centuries. The main periodicities present in the TL profile are studied and the similarities between the TL variations and the fluctuations in the contemporary tree-ring A 14 C signal are considered. An interesting result is the presence, in the TL data, of a well-defined 11-year cycle which is stable and ‘in phase’ for the entire period analysed. We also discuss how four dominant periodicities present in the TL data may be rewritten as the sum of an 11.4-year and of an 82.6- year cycle (reminiscent respectively of the Schwabe and of the Gleissberg cycles of solar activity), which are both amplitude modulated by a 206-year wave. This last periodicity has already been shown to play a dominant role in the A 14 C record. These results suggest that the TL profiles of recent marine sediments may be successfully used as a new line of evidence for solar variability in the past centuries.

scholarly journals Anaerobic microbial degradation of protein and lipid macromolecules in subarctic marine sediment

2020 ◽  
Author(s):  
Claus Pelikan ◽  
Kenneth Wasmund ◽  
Clemens Glombitza ◽  
Bela Hausmann ◽  
Craig W. Herbold ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Marine Sediment ◽  
Volatile Fatty Acids ◽  
Degradation Products ◽  
Stable Isotope Probing ◽  
Rrna Gene ◽  
Genomic Features ◽  
Carbon Processing ◽  
Functional Partitioning

AbstractMicroorganisms in marine sediments play major roles in marine biogeochemical cycles by mineralizing substantial quantities of organic matter from decaying cells. Proteins and lipids are abundant components of necromass, yet microorganisms that degrade them remain understudied. Here, we revealed identities, trophic interactions and genomic features of microorganisms that degraded 13C-labelled proteins and lipids in cold anoxic microcosms with sulfidic subarctic marine sediment. Supplemented proteins and lipids were rapidly fermented to various volatile fatty acids within five days. DNA-stable isotope probing (SIP) suggested Psychrilyobacter atlanticus was an important primary degrader of proteins, and Psychromonas members were important primary degraders of both proteins and lipids. Closely related Psychromonas populations, as represented by distinct 16S rRNA gene variants, differentially utilized either proteins or lipids. DNA-SIP also showed 13C-labeling of various Deltaproteobacteria within ten days, indicating trophic transfer of carbon to putative sulfate-reducers. Metagenome-assembled genomes revealed the primary hydrolyzers encoded secreted peptidases or lipases, and enzymes for catabolism of protein or lipid degradation products. Psychromonas were prevalent in diverse marine sediments, suggesting they are important players in organic carbon processing in situ. Together, this study provides an improved understanding of the metabolic processes and functional partitioning of necromass macromolecules among microorganisms in the seafloor.

scholarly journals DISTRIBUSI SPASIAL FORAMINIFERA DI PERAIRAN TELUK CENDERAWASIH, PAPUA BARAT

2020 ◽  
Vol 17 (2) ◽  
Author(s):  
Eko Saputro ◽  
Lili Fauzielly ◽  
Imelda Rosalina Silalahi ◽  
Winatris Winatris
Keyword(s):  
Spatial Distribution ◽  
Community Structure ◽  
Marine Sediments ◽  
Marine Sediment ◽  
Benthic Foraminifera ◽  
Planktonic Foraminifera ◽  
Sediment Samples ◽  
Enclosed Bay ◽  
Papua Barat ◽  
Good Environment

Sebanyak 20 sampel sedimen dari perairan Teluk Cenderawasih telah digunakan sebagai bahan studi foraminifera, yang bertujuan untuk mengetahui bagaimana sebaran spasial dan struktur komunitas foraminifera di perairan Teluk Cenderawasih. Hasil penelitian menunjukkan komposisi foraminifera planktonik yang terdiri dari 7 Genus dan 13 Spesies sedangkan foraminifera bentonik terdiri dari 57 Genus dan 87 Spesies. Foraminifera planktonik yang paling umum ditemukan karena muncul di seluruh sampel adalah genus Globigerinoides, terutama G. trilobus dan G. ruber. Sedangkan foraminifera bentonik didominasi oleh subordo Rotaliina, dan yang paling banyak ditemukan adalah genus Cibicidiodes dan Lenticulina. Keanekaragaman foraminifera planktonik dan bentonik termasuk dalam kategori tinggi dengan kisaran antara 0.82 – 0.90 (planktonik) dan 0.79 – 0.95 (bentonik). Kemerataan foraminifera planktonik dan bentonik juga termasuk dalam kategori tinggi dengan kisaran antara 0.83 – 0.99 (planktonik) dan 0.82–0.99 (bentonik). Sedangkan untuk dominasi foraminifera planktonik dan bentonik berada dalam kategori rendah dengan kisaran 0.10 – 0.18 (planktonik) dan 0.05 – 0.21 (bentonik). Hal ini menunjukkan bahwa Teluk Cendrawasih meskipun merupakan perairan yang semi tertutup, namun kondisinya masih sangat bagus bagi perkembangan foraminiferaKata Kunci : foraminifera, distribusi spasial, struktur komunitas, dan Teluk Cenderawasih A total of 20 marine sediment samples from Cenderawasih Bay waters have been used for foraminiferal study, . The purpose to describe the spatial distribution and structure of the foraminifera community in the waters of Cenderawasih Bay. The results indicate that marine sediments are composed of 7 genera and 13 species of planktonic foraminifera, and 57 genera and 87 species belong to benthic foraminifera. The most common planktonic foraminifera is Globigerinoides which is found in all location, particularly G. trilobus and G. ruber. Furthermore, benthonic foraminifera is dominated by subordo Rotaliina, particularly genera Cibicidoides and Lenticulina as the most common genera. Diversity of both Planktonic and benthonic foraminifera are categorized as high, the values are between 0.82 and 0.90, and between 0.79 and 0.95 respectively. Planktonic and benthonic foraminiferal evenness are also high with range value between 0.83 and 0.99 (planktonic), and between 0.82 and 0.99 (benthonic). In contrast, dominance of both foraminiferal type are low, between 0.10 and 0.18 for planktonic, and between 0.05 and 0.21 (benthonic).This indicates that despite a semi–enclosed bay, Cendrawasih Bay is still considered as a good environment for foraminiferal community. Keywords: foraminifera, spatial distribution, community structure, and Cenderawasih Bay.

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