{"id":67,"date":"2020-07-15T12:50:38","date_gmt":"2020-07-15T12:50:38","guid":{"rendered":"https:\/\/students.pingry.org\/irt\/?page_id=67"},"modified":"2020-08-23T05:00:20","modified_gmt":"2020-08-23T05:00:20","slug":"metagenomics","status":"publish","type":"page","link":"https:\/\/students.pingry.org\/irt\/metagenomics\/","title":{"rendered":"Metagenomics"},"content":{"rendered":"

[et_pb_section fb_built=”1″ admin_label=”Hero” _builder_version=”3.22″ background_color=”#f8fbfe” use_background_color_gradient=”on” background_color_gradient_start=”#53a0fd” background_color_gradient_end=”#4161d4″ background_color_gradient_direction=”135deg” background_image=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/07\/geometric-bg-overlay-01.jpg” background_blend=”overlay” custom_padding=”8.6%|0px||0px||” animation_style=”zoom” animation_direction=”bottom” animation_intensity_zoom=”8%” animation_starting_opacity=”100%” box_shadow_style=”preset7″ box_shadow_horizontal=”0px” box_shadow_vertical=”-200px” box_shadow_color=”#F8FBFE”][et_pb_row _builder_version=”3.25″][et_pb_column type=”4_4″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.4.7″ text_font=”Abhaya Libre||||||||” text_text_color=”#ffffff” text_font_size=”18px” text_line_height=”1.8em” header_font=”Abhaya Libre|700|||||||” header_text_align=”center” header_text_color=”#ffffff” header_font_size=”45px” header_line_height=”1.3em” header_2_font=”||||||||” text_orientation=”center” max_width=”700px” module_alignment=”center” custom_margin=”||18px|||” custom_padding=”||17px|||” inline_fonts=”Abhaya Libre”]<\/p>\n

Characterizing microbial community structure, dynamics, and succession in composters using metagenomics<\/span><\/h1>\n

[\/et_pb_text][et_pb_text _builder_version=”4.4.7″ header_font=”Abhaya Libre||||||||” header_3_font=”Abhaya Libre|600|||||||” header_3_text_color=”#ffffff” header_3_font_size=”25px” custom_margin=”||60px|||” header_3_text_shadow_style=”preset5″]<\/p>\n

Ryan Arrazcaeta, Ainsely Ellison, Dr. Sparrow<\/h3>\n

[\/et_pb_text][et_pb_image align=”center” align_tablet=”center” align_phone=”” align_last_edited=”on|desktop” _builder_version=”4.4.7″ custom_margin=”41px|||||” custom_padding=”||45px|||” border_radii=”on|10px|10px|10px|10px” border_width_all=”1px” border_color_all=”rgba(51,51,51,0.1)” box_shadow_style=”preset1″ box_shadow_vertical=”10px” box_shadow_blur=”30px” box_shadow_color=”rgba(34,56,101,0.09)”][\/et_pb_image][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.4.7″][et_pb_column type=”4_4″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ text_font=”Abhaya Libre|600|||||||” header_font_size=”54px”]<\/p>\n

Project Summary<\/h1>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”Features” _builder_version=”3.22″ background_color=”#f8fbfe” custom_margin=”-62px|||||” custom_padding=”151px|0px|100px|0px||”][et_pb_row _builder_version=”4.4.7″ min_height=”135px”][et_pb_column type=”4_4″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ text_font=”Abhaya Libre||||||||” text_text_color=”#ffffff” text_line_height=”1.9em” background_color=”#88c4dd” custom_margin=”-143px|||||” custom_padding=”14px||0px||false|false”]<\/p>\n

This project is dependent upon, and is being conducted in collaboration with, Ms. Olivia Tandon and the Composter Team.<\/span><\/h3>\n

Continuous drum-style composters contain diverse microbiomes which are crucial to nutrient cycling. Recent advancements in next-generation sequencing (NGS) technology have created unprecedented opportunities to characterize diverse microbial communities in complex environments. In combining time-course sampling with NGS technology, we can create a detailed \u201cfamily portrait\u201d of the composter microbiome. We also expect that sampling at multiple points within a composter will allow for comparisons between population profiles over time. These analyses will contribute a rich body of data to the comparatively new field of metagenomics. Finally, the sequencing of novel genomes may uncover microbes in biomass degradation that invite further research, such as in biochemical catalysis and biofuel production. A thorough characterization of the microbial communities in a composter would be both a project in general microbiology and an applied research investigation to improve our understanding of modern composters and operational efficiency.<\/span><\/h3>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ _builder_version=”4.4.7″][et_pb_column type=”1_2″ _builder_version=”4.4.7″][et_pb_image src=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/08\/composter.jpg” title_text=”composter” _builder_version=”4.4.7″ width=”100%”][\/et_pb_image][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_2_font=”Abhaya Libre||||||||” background_color=”#d6d6d6″ width=”79%” custom_margin=”||0px||false|false” custom_padding=”|0px|0px||false|false”]<\/p>\n

Pingry composter with student, Ryan Arrazcaeta ’22, for scale.<\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.4.7″][et_pb_column type=”4_4″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ text_font=”|600|on||||||” header_font_size=”53px” inline_fonts=”Abhaya Libre”]<\/p>\n

Four Main Objectives:<\/span><\/h1>\n

[\/et_pb_text][et_pb_text _builder_version=”4.4.7″ text_font=”Abhaya Libre||||||||” background_color=”#88c4dd” custom_margin=”|-9px||||” custom_padding=”20px|14px|8px|12px|false|false”]<\/p>\n

This is a descriptive biology project that aims to identify the microbial communities present within a composter during startup and transition to a thermophilic regime. In doing so, this project aims to achieve four objectives:<\/span><\/h3>\n

1. Identify the presence and relative abundance of various microbial communities (bacteria, fungi, and archaea) present in a composter using next-generation sequencing as a composter starts up and its operating parameters change<\/h3>\n

<\/h3>\n

2. Conduct physiochemical analyses to correlate changes in operating parameters to microbial community shifts<\/h3>\n

<\/h3>\n

3. Identify and sequence novel species that are believed to play meaningful roles in composting\/biomass decomposition after bioinformatic analysis<\/h3>\n

<\/h3>\n

4. Describe the niches of different microbes in composters and their interactions with each other<\/h3>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row admin_label=”Tittle” _builder_version=”3.25″][et_pb_column type=”4_4″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text _builder_version=”3.27.4″ text_font=”Nunito Sans||||||||” text_text_color=”#959baf” text_font_size=”18px” text_line_height=”1.8em” header_font=”||||||||” header_text_align=”center” header_text_color=”#535b7c” header_2_font=”Nunito Sans|700|||||||” header_2_text_color=”#535b7c” header_2_font_size=”35px” header_2_line_height=”1.3em” text_orientation=”center” max_width=”700px” module_alignment=”center”]<\/p>\n

<\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.4.7″ min_height=”0px” custom_margin=”-22px|auto||auto||”][et_pb_column type=”4_4″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_font=”Abhaya Libre|600|||||||” header_2_font=”Abhaya Libre|600|||||||” header_2_font_size=”53px”]<\/p>\n

Current State<\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ _builder_version=”4.4.7″][et_pb_column type=”1_2″ _builder_version=”4.4.7″][et_pb_image src=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/08\/metaGgel-1.png” title_text=”metaGgel” _builder_version=”4.4.7″ width=”100%” max_width=”100%” height=”507px”][\/et_pb_image][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_font=”Abhaya Libre||||||||” background_color=”#d6d6d6″]<\/p>\n

Figure 1.<\/strong> Agarose gel quality control. NGS requires long fragments for analysis, and streaks that are denser at the top of the gel are a positive sign; B1 and B2 are indicative of poor DNA extraction.<\/span><\/h1>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.4.7″][et_pb_column type=”4_4″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ text_font=”Abhaya Libre||||||||” header_letter_spacing=”1px” background_color=”#88c4dd” custom_margin=”||56px|||” custom_padding=”15px||8px||false|false”]<\/p>\n

The Metagenomics Research Group was formed in 2019 and is an ongoing project. In recent months, we have studied the growing body of literature in the field of metagenomics. We have further begun to outline long-term project goals and protocols, in addition to conducting a series of preliminary trials. A pilot proof-of-concept trial confirmed our protocol\u2019s reproducibility and produced reasonable results that can contribute to baseline data for future trials. Our initial analysis of composter DNA suggested the presence of previously uncharacterized species, and deeper sequencing of the DNA samples may allow for the identification and characterization of such species. Discoveries of this type have occurred following the bioinformatic analysis of microbial communities in naturally-occurring microbiomes.\u00a0 Due to the projected expenses of the project, we have worked towards securing funding from in-school and out-of-school grants.<\/span><\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ _builder_version=”4.4.7″][et_pb_column type=”1_2″ _builder_version=”4.4.7″][et_pb_image src=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/08\/NGS1-2.png” title_text=”NGS1″ _builder_version=”4.4.7″][\/et_pb_image][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.4.7″][et_pb_image src=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/08\/NGS2.png” title_text=”NGS2″ _builder_version=”4.4.7″][\/et_pb_image][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_2,1_2″ _builder_version=”4.4.7″ min_height=”94px”][et_pb_column type=”1_2″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_font=”Abhaya Libre||||||||” header_2_font=”Abhaya Libre||||||||”]<\/p>\n

Figure 2. Example of NGS results for bacterial families.<\/span><\/h2>\n

[\/et_pb_text][et_pb_text _builder_version=”4.4.7″ header_font=”Abhaya Libre|600|||||||” header_2_font=”Abhaya Libre|600|||||||” header_2_font_size=”54px” inline_fonts=”Abhaya Libre”]<\/p>\n

Next Steps<\/span><\/h2>\n

[\/et_pb_text][\/et_pb_column][et_pb_column type=”1_2″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_2_font=”Abhaya Libre||||||||”]<\/p>\n

Figure 3. Example of NGS results for fungal families<\/span><\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.4.7″][et_pb_column type=”4_4″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_2_font=”Abhaya Libre||||||||” header_2_letter_spacing=”1px” background_color=”#88c4dd”]<\/p>\n

This project is still in its infancy. In the coming months, composter contents will be sampled from various points in the cylinder and at various times during the year. Temperature inside the composter will be monitored continuously using a submersible data logger. Samples will be analyzed for pH, moisture content, and carbon\/nitrogen ratio. DNA will be isolated from dried and sifted samples and subjected to NGS of the generally accepted \u201cbarcode\u201d genes 16S ribosomal RNA (for bacteria and archaea) and the ribosomal ITS sequence (for fungi). DNA will be isolated and assessed for quality at Pingry, while DNA sequencing and initial bioinformatic analysis will be outsourced to a contract lab.<\/span><\/h2>\n

<\/h2>\n

Composter conditions will vary based on feedstock, position down the length of the composter, and time of year. Correlations will be sought between operating parameters and the microbial communities identified. The resulting data allow for longitudinal and cross-sectional comparisons through bioinformatic analyses. Special attention will be focused on (1) microbial communities that correlate with efficient composting and (2) the identification of novel species so as to create a cohesive \u201cnarrative\u201d of the composter microbiome using sequencing results.<\/span><\/h2>\n

<\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”Center Aligned Text ” _builder_version=”4.4.7″ background_color=”#f8fbfe” use_background_color_gradient=”on” background_color_gradient_start=”#53a0fd” background_color_gradient_end=”#4161d4″ background_color_gradient_direction=”135deg” background_image=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/07\/geometric-bg-overlay-02.jpg” background_blend=”overlay” custom_padding=”100px|0px|100px|0px” animation_style=”zoom” animation_direction=”bottom” animation_intensity_zoom=”8%” animation_starting_opacity=”100%”][et_pb_row admin_label=”Tittle” _builder_version=”3.25″][et_pb_column type=”4_4″ _builder_version=”3.25″ custom_padding=”|||” custom_padding__hover=”|||”][et_pb_text _builder_version=”4.4.7″ header_font=”Abhaya Libre|700|||||||” header_text_align=”center” header_text_color=”#ffffff” header_font_size=”60px”]<\/p>\n

Meet the Team<\/h1>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.4.7″ column_structure=”1_3,1_3,1_3″][et_pb_column _builder_version=”4.4.7″ type=”1_3″][et_pb_image src=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/08\/Arrazcaeta_Ryan_Grade-10_2019-20.jpg” _builder_version=”4.4.7″ title_text=”Arrazcaeta_Ryan_Grade 10_2019-20″ hover_enabled=”0″][\/et_pb_image][\/et_pb_column][et_pb_column _builder_version=”4.4.7″ type=”1_3″][et_pb_image src=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/08\/Ellison_Ainsley_Grade-10_2019-20.jpg” _builder_version=”4.4.7″ title_text=”Ellison_Ainsley_Grade 10_2019-20″ hover_enabled=”0″][\/et_pb_image][\/et_pb_column][et_pb_column _builder_version=”4.4.7″ type=”1_3″][et_pb_image src=”https:\/\/students.pingry.org\/irt\/wp-content\/uploads\/sites\/19\/2020\/08\/Sparrow_Carl_cropped.jpg” _builder_version=”4.4.7″ title_text=”Sparrow_Carl_cropped” hover_enabled=”0″][\/et_pb_image][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_3,1_3,1_3″ _builder_version=”4.4.7″][et_pb_column type=”1_3″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_2_font=”Abhaya Libre|600|||||||” header_2_text_color=”#ffffff” header_2_font_size=”35px”]<\/p>\n

Ryan Arrazcaeta<\/h2>\n

[\/et_pb_text][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_font=”Abhaya Libre|600|||||||” header_text_align=”center” header_text_color=”#ffffff” header_2_font=”Abhaya Libre|600|||||||” header_2_text_color=”#ffffff” header_2_font_size=”35px” header_2_letter_spacing=”1px”]<\/p>\n

Ainsley Ellison<\/h2>\n

[\/et_pb_text][\/et_pb_column][et_pb_column type=”1_3″ _builder_version=”4.4.7″][et_pb_text _builder_version=”4.4.7″ header_font=”Abhaya Libre|600|||||||” header_2_font=”Abhaya Libre|600|||||||” header_2_text_color=”#ffffff” header_2_font_size=”35px”]<\/p>\n

Dr. Sparrow<\/h2>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ _builder_version=”4.4.7″][\/et_pb_section]<\/p>\n","protected":false},"excerpt":{"rendered":"

Characterizing microbial community structure, dynamics, and succession in composters using metagenomicsRyan Arrazcaeta, Ainsely Ellison, Dr. SparrowProject SummaryThis project is dependent upon, and is being conducted in collaboration with, Ms. Olivia Tandon and the Composter Team. Continuous drum-style composters contain diverse microbiomes which are crucial to nutrient cycling. Recent advancements in next-generation sequencing (NGS) technology have […]<\/p>\n","protected":false},"author":42,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-67","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/students.pingry.org\/irt\/wp-json\/wp\/v2\/pages\/67","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/students.pingry.org\/irt\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/students.pingry.org\/irt\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/students.pingry.org\/irt\/wp-json\/wp\/v2\/users\/42"}],"replies":[{"embeddable":true,"href":"https:\/\/students.pingry.org\/irt\/wp-json\/wp\/v2\/comments?post=67"}],"version-history":[{"count":4,"href":"https:\/\/students.pingry.org\/irt\/wp-json\/wp\/v2\/pages\/67\/revisions"}],"predecessor-version":[{"id":182,"href":"https:\/\/students.pingry.org\/irt\/wp-json\/wp\/v2\/pages\/67\/revisions\/182"}],"wp:attachment":[{"href":"https:\/\/students.pingry.org\/irt\/wp-json\/wp\/v2\/media?parent=67"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}